Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13508:7318:3065 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13508:7318:3065 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:22602:26712:5749 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:22602:26712:5749 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:22607:7176:15645 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:22607:7176:15645 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:23403:5485:5886 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:23403:5485:5886 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:23407:2398:3530 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:23407:2398:3530 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11102:22446:4818 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11102:22446:4818 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12312:1402:10624 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12312:1402:10624 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:13206:11371:11769 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:13206:11371:11769 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:13206:23035:11461 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:13206:23035:11461 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21101:8936:19871 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21101:8936:19871 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21203:5165:8763 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21203:5165:8763 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:23308:6331:15479 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:23308:6331:15479 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12508:3076:5604 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12508:3076:5604 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12611:25808:12921 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12611:25808:12921 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13608:9002:18989 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13608:9002:18989 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21409:13066:16971 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21409:13066:16971 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22507:7441:3878 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22507:7441:3878 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11205:21717:10374 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11205:21717:10374 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:21302:13378:2723 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:21302:13378:2723 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:22103:4611:15488 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:22103:4611:15488 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:22111:7915:18974 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:22111:7915:18974 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:23111:21035:15550 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:23111:21035:15550 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:23203:11376:1439 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:23203:11376:1439 2:N:0:GTCTTAGT' because it was < 2 characters long
2145498 reads; of these:
  2145498 (100.00%) were paired; of these:
    284839 (13.28%) aligned concordantly 0 times
    305559 (14.24%) aligned concordantly exactly 1 time
    1555100 (72.48%) aligned concordantly >1 times
    ----
    284839 pairs aligned concordantly 0 times; of these:
      5379 (1.89%) aligned discordantly 1 time
    ----
    279460 pairs aligned 0 times concordantly or discordantly; of these:
      558920 mates make up the pairs; of these:
        395162 (70.70%) aligned 0 times
        13562 (2.43%) aligned exactly 1 time
        150196 (26.87%) aligned >1 times
90.79% overall alignment rate
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:11407:16789:5873 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:11407:16789:5873 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13501:5766:13903 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13501:5766:13903 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13601:8419:14985 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13601:8419:14985 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13610:1537:4689 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13610:1537:4689 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21408:12748:8491 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21408:12748:8491 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21411:19488:9938 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21411:19488:9938 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21506:20948:13593 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21506:20948:13593 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21511:24211:15423 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21511:24211:15423 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:23611:19558:18788 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:23611:19558:18788 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:23611:26067:18967 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:23611:26067:18967 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11204:14162:1362 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11204:14162:1362 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11204:14546:18636 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11204:14546:18636 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12103:6895:16268 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12103:6895:16268 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12105:10054:5138 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12105:10054:5138 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12105:22544:8398 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12105:22544:8398 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12111:8656:9008 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12111:8656:9008 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12208:1434:17301 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12208:1434:17301 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:13101:24552:5957 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:13101:24552:5957 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:13105:6843:11447 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:13105:6843:11447 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:13207:24572:2373 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:13207:24572:2373 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:13305:5404:5979 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:13305:5404:5979 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21108:4602:8782 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21108:4602:8782 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21307:23458:18989 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21307:23458:18989 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:22101:4504:15220 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:22101:4504:15220 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:22212:22622:1317 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:22212:22622:1317 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:22307:16274:3412 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:22307:16274:3412 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:23309:17664:2868 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:23309:17664:2868 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11411:9883:14965 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11411:9883:14965 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11603:21423:2735 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11603:21423:2735 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11605:11272:10103 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11605:11272:10103 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11611:16875:7563 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11611:16875:7563 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12405:14493:8303 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12405:14493:8303 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12506:5781:5886 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12506:5781:5886 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12511:21645:14677 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12511:21645:14677 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12603:22172:15920 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12603:22172:15920 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12604:11975:4638 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12604:11975:4638 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13403:10317:4268 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13403:10317:4268 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13407:24126:4134 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13407:24126:4134 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13502:1541:17071 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13502:1541:17071 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13503:21304:19153 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13503:21304:19153 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13609:9793:10883 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13609:9793:10883 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22610:25368:3853 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22610:25368:3853 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23401:18515:16780 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23401:18515:16780 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23402:11083:5468 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23402:11083:5468 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23403:20039:2339 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23403:20039:2339 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23405:15927:8167 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23405:15927:8167 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23503:5788:3723 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23503:5788:3723 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23507:9203:4463 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23507:9203:4463 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23611:8676:17263 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23611:8676:17263 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11109:24303:4583 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11109:24303:4583 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11202:6075:3018 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11202:6075:3018 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:12206:12414:12925 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:12206:12414:12925 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:13308:16869:15688 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:13308:16869:15688 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:22301:13135:7233 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:22301:13135:7233 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:23305:11938:1425 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:23305:11938:1425 2:N:0:GTCTTAGT' because it was < 2 characters long
4282240 reads; of these:
  4282240 (100.00%) were paired; of these:
    621973 (14.52%) aligned concordantly 0 times
    792029 (18.50%) aligned concordantly exactly 1 time
    2868238 (66.98%) aligned concordantly >1 times
    ----
    621973 pairs aligned concordantly 0 times; of these:
      14421 (2.32%) aligned discordantly 1 time
    ----
    607552 pairs aligned 0 times concordantly or discordantly; of these:
      1215104 mates make up the pairs; of these:
        860920 (70.85%) aligned 0 times
        34745 (2.86%) aligned exactly 1 time
        319439 (26.29%) aligned >1 times
89.95% overall alignment rate
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:12409:19765:12839 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:12409:19765:12839 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:12511:8475:9570 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:12511:8475:9570 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13407:18372:17952 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13407:18372:17952 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13607:6957:4808 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13607:6957:4808 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13609:23863:11691 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13609:23863:11691 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13611:25124:19684 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13611:25124:19684 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:23406:9456:18279 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:23406:9456:18279 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11101:26362:3635 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11101:26362:3635 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11112:16842:6048 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11112:16842:6048 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11202:14891:19695 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11202:14891:19695 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11301:17208:12740 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11301:17208:12740 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11310:25678:13998 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11310:25678:13998 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12109:10457:8520 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12109:10457:8520 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12109:13093:9689 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12109:13093:9689 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12111:25909:16640 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12111:25909:16640 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12305:26007:8917 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12305:26007:8917 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12309:12163:17242 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12309:12163:17242 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:13108:15149:9324 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:13108:15149:9324 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21211:19127:7342 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21211:19127:7342 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21212:15469:14677 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21212:15469:14677 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:22304:11254:18975 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:22304:11254:18975 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:23208:8086:19752 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:23208:8086:19752 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:23305:6288:5137 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:23305:6288:5137 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11408:24532:7624 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11408:24532:7624 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11412:25253:9848 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11412:25253:9848 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11503:24668:13031 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11503:24668:13031 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11504:2730:10615 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11504:2730:10615 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11512:16136:13033 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11512:16136:13033 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12407:14155:11596 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12407:14155:11596 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12412:13181:11936 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12412:13181:11936 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12612:19562:17181 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12612:19562:17181 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13401:26787:18899 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13401:26787:18899 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13408:14194:13901 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13408:14194:13901 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21405:24949:13409 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21405:24949:13409 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21407:9333:3302 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21407:9333:3302 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21503:19159:19230 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21503:19159:19230 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21505:12431:9887 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21505:12431:9887 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21507:24440:20309 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21507:24440:20309 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21608:18877:11802 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21608:18877:11802 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21608:8033:9916 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21608:8033:9916 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22401:12434:9418 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22401:12434:9418 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22408:9812:8927 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22408:9812:8927 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22510:25091:5368 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22510:25091:5368 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22511:20977:17809 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22511:20977:17809 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23509:26738:10209 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23509:26738:10209 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23606:15190:12814 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23606:15190:12814 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23609:7281:1299 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23609:7281:1299 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11102:2181:7272 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11102:2181:7272 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11105:20806:15262 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11105:20806:15262 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11105:7779:1221 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11105:7779:1221 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11112:11506:1663 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11112:11506:1663 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11209:10444:3968 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11209:10444:3968 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:13103:2743:13127 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:13103:2743:13127 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:13112:20403:1793 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:13112:20403:1793 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:13309:21108:13738 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:13309:21108:13738 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:21108:7704:3832 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:21108:7704:3832 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:21211:25819:9829 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:21211:25819:9829 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:21302:24534:6039 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:21302:24534:6039 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:21306:19593:3321 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:21306:19593:3321 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:21307:23971:8360 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:21307:23971:8360 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:21310:25043:5091 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:21310:25043:5091 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:23102:21231:7526 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:23102:21231:7526 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:23312:17918:1207 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:23312:17918:1207 2:N:0:GTCTTAGT' because it was < 2 characters long
3904073 reads; of these:
  3904073 (100.00%) were paired; of these:
    3559324 (91.17%) aligned concordantly 0 times
    44008 (1.13%) aligned concordantly exactly 1 time
    300741 (7.70%) aligned concordantly >1 times
    ----
    3559324 pairs aligned concordantly 0 times; of these:
      781 (0.02%) aligned discordantly 1 time
    ----
    3558543 pairs aligned 0 times concordantly or discordantly; of these:
      7117086 mates make up the pairs; of these:
        6981299 (98.09%) aligned 0 times
        4049 (0.06%) aligned exactly 1 time
        131738 (1.85%) aligned >1 times
10.59% overall alignment rate
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:11602:9846:19420 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:11602:9846:19420 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:12406:3024:15092 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:12406:3024:15092 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13405:14093:16763 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13405:14093:16763 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13609:26350:6994 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:13609:26350:6994 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21408:3594:2122 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21408:3594:2122 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21411:17631:20335 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21411:17631:20335 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21508:10236:12501 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21508:10236:12501 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21509:23366:6483 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21509:23366:6483 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21605:5254:1105 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21605:5254:1105 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21610:15864:3462 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:21610:15864:3462 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:22412:8294:7469 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:22412:8294:7469 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:22612:2202:7526 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:22612:2202:7526 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:23509:24961:10402 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:23509:24961:10402 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:23612:6198:10922 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:3:23612:6198:10922 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11101:8284:12438 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11101:8284:12438 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11206:12691:13664 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11206:12691:13664 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11206:14285:2308 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11206:14285:2308 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11305:16478:2510 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11305:16478:2510 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11305:23190:2426 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:11305:23190:2426 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12107:1995:19188 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12107:1995:19188 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12212:24981:4779 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:12212:24981:4779 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:13102:8665:17423 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:13102:8665:17423 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21106:15901:4411 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21106:15901:4411 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21201:22352:16219 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21201:22352:16219 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21203:13143:19235 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21203:13143:19235 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21209:19408:19035 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21209:19408:19035 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21209:25968:16232 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21209:25968:16232 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21210:12120:9587 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21210:12120:9587 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21210:14858:10411 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21210:14858:10411 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21210:15053:11546 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21210:15053:11546 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21312:16394:4545 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:21312:16394:4545 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:22110:10370:6645 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:22110:10370:6645 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:22205:1375:15885 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:22205:1375:15885 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:22208:26749:9709 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:22208:26749:9709 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:23212:1660:17289 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:23212:1660:17289 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:23302:22854:8910 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:23302:22854:8910 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:23305:16457:5609 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:1:23305:16457:5609 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11409:24302:7634 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11409:24302:7634 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11602:3681:8940 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11602:3681:8940 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11605:23230:4471 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:11605:23230:4471 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12602:4017:10666 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12602:4017:10666 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12605:10646:14408 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:12605:10646:14408 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13404:20129:9749 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13404:20129:9749 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13404:7417:8059 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13404:7417:8059 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13506:23958:1654 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:13506:23958:1654 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21411:17373:9425 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21411:17373:9425 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21503:5922:3656 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21503:5922:3656 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21601:7292:11349 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:21601:7292:11349 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22405:16974:6802 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22405:16974:6802 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22505:26097:7354 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22505:26097:7354 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22506:23690:17229 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22506:23690:17229 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22507:21968:19825 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:22507:21968:19825 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23501:1715:12077 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23501:1715:12077 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23603:22224:10928 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:4:23603:22224:10928 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11104:10947:15925 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11104:10947:15925 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11105:17360:8484 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11105:17360:8484 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11201:3819:19415 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11201:3819:19415 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11211:15961:15679 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:11211:15961:15679 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:12209:1650:14700 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:12209:1650:14700 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:13103:9980:3139 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:13103:9980:3139 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:13106:24053:5932 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:13106:24053:5932 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:13201:20330:1498 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:13201:20330:1498 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:21302:2833:12977 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:21302:2833:12977 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:21311:14258:9458 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:21311:14258:9458 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:22202:3837:12185 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:22202:3837:12185 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:22301:20556:17289 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:22301:20556:17289 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:22307:19451:12536 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:22307:19451:12536 2:N:0:GTCTTAGT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:23104:19762:16516 2:N:0:GTCTTAGT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HHNFTBGX5180320:HHNFTBGX5:2:23104:19762:16516 2:N:0:GTCTTAGT' because it was < 2 characters long
4112565 reads; of these:
  4112565 (100.00%) were paired; of these:
    3471773 (84.42%) aligned concordantly 0 times
    85092 (2.07%) aligned concordantly exactly 1 time
    555700 (13.51%) aligned concordantly >1 times
    ----
    3471773 pairs aligned concordantly 0 times; of these:
      992 (0.03%) aligned discordantly 1 time
    ----
    3470781 pairs aligned 0 times concordantly or discordantly; of these:
      6941562 mates make up the pairs; of these:
        6773824 (97.58%) aligned 0 times
        5633 (0.08%) aligned exactly 1 time
        162105 (2.34%) aligned >1 times
17.64% overall alignment rate
2967 GFF lines processed.
100000 SAM alignment record pairs processed.
200000 SAM alignment record pairs processed.
300000 SAM alignment record pairs processed.
400000 SAM alignment record pairs processed.
500000 SAM alignment record pairs processed.
600000 SAM alignment record pairs processed.
700000 SAM alignment record pairs processed.
800000 SAM alignment record pairs processed.
900000 SAM alignment record pairs processed.
1000000 SAM alignment record pairs processed.
1100000 SAM alignment record pairs processed.
1200000 SAM alignment record pairs processed.
1300000 SAM alignment record pairs processed.
1400000 SAM alignment record pairs processed.
1500000 SAM alignment record pairs processed.
1600000 SAM alignment record pairs processed.
1700000 SAM alignment record pairs processed.
1800000 SAM alignment record pairs processed.
1900000 SAM alignment record pairs processed.
2000000 SAM alignment record pairs processed.
2100000 SAM alignment record pairs processed.
2145498 SAM alignment pairs processed.
2967 GFF lines processed.
100000 SAM alignment record pairs processed.
200000 SAM alignment record pairs processed.
300000 SAM alignment record pairs processed.
400000 SAM alignment record pairs processed.
500000 SAM alignment record pairs processed.
600000 SAM alignment record pairs processed.
700000 SAM alignment record pairs processed.
800000 SAM alignment record pairs processed.
900000 SAM alignment record pairs processed.
1000000 SAM alignment record pairs processed.
1100000 SAM alignment record pairs processed.
1200000 SAM alignment record pairs processed.
1300000 SAM alignment record pairs processed.
1400000 SAM alignment record pairs processed.
1500000 SAM alignment record pairs processed.
1600000 SAM alignment record pairs processed.
1700000 SAM alignment record pairs processed.
1800000 SAM alignment record pairs processed.
1900000 SAM alignment record pairs processed.
2000000 SAM alignment record pairs processed.
2100000 SAM alignment record pairs processed.
2200000 SAM alignment record pairs processed.
2300000 SAM alignment record pairs processed.
2400000 SAM alignment record pairs processed.
2500000 SAM alignment record pairs processed.
2600000 SAM alignment record pairs processed.
2700000 SAM alignment record pairs processed.
2800000 SAM alignment record pairs processed.
2900000 SAM alignment record pairs processed.
3000000 SAM alignment record pairs processed.
3100000 SAM alignment record pairs processed.
3200000 SAM alignment record pairs processed.
3300000 SAM alignment record pairs processed.
3400000 SAM alignment record pairs processed.
3500000 SAM alignment record pairs processed.
3600000 SAM alignment record pairs processed.
3700000 SAM alignment record pairs processed.
3800000 SAM alignment record pairs processed.
3900000 SAM alignment record pairs processed.
4000000 SAM alignment record pairs processed.
4100000 SAM alignment record pairs processed.
4200000 SAM alignment record pairs processed.
4282240 SAM alignment pairs processed.
2967 GFF lines processed.
100000 SAM alignment record pairs processed.
200000 SAM alignment record pairs processed.
300000 SAM alignment record pairs processed.
400000 SAM alignment record pairs processed.
500000 SAM alignment record pairs processed.
600000 SAM alignment record pairs processed.
700000 SAM alignment record pairs processed.
800000 SAM alignment record pairs processed.
900000 SAM alignment record pairs processed.
1000000 SAM alignment record pairs processed.
1100000 SAM alignment record pairs processed.
1200000 SAM alignment record pairs processed.
1300000 SAM alignment record pairs processed.
1400000 SAM alignment record pairs processed.
1500000 SAM alignment record pairs processed.
1600000 SAM alignment record pairs processed.
1700000 SAM alignment record pairs processed.
1800000 SAM alignment record pairs processed.
1900000 SAM alignment record pairs processed.
2000000 SAM alignment record pairs processed.
2100000 SAM alignment record pairs processed.
2200000 SAM alignment record pairs processed.
2300000 SAM alignment record pairs processed.
2400000 SAM alignment record pairs processed.
2500000 SAM alignment record pairs processed.
2600000 SAM alignment record pairs processed.
2700000 SAM alignment record pairs processed.
2800000 SAM alignment record pairs processed.
2900000 SAM alignment record pairs processed.
3000000 SAM alignment record pairs processed.
3100000 SAM alignment record pairs processed.
3200000 SAM alignment record pairs processed.
3300000 SAM alignment record pairs processed.
3400000 SAM alignment record pairs processed.
3500000 SAM alignment record pairs processed.
3600000 SAM alignment record pairs processed.
3700000 SAM alignment record pairs processed.
3800000 SAM alignment record pairs processed.
3900000 SAM alignment record pairs processed.
3904073 SAM alignment pairs processed.
2967 GFF lines processed.
100000 SAM alignment record pairs processed.
200000 SAM alignment record pairs processed.
300000 SAM alignment record pairs processed.
400000 SAM alignment record pairs processed.
500000 SAM alignment record pairs processed.
600000 SAM alignment record pairs processed.
700000 SAM alignment record pairs processed.
800000 SAM alignment record pairs processed.
900000 SAM alignment record pairs processed.
1000000 SAM alignment record pairs processed.
1100000 SAM alignment record pairs processed.
1200000 SAM alignment record pairs processed.
1300000 SAM alignment record pairs processed.
1400000 SAM alignment record pairs processed.
1500000 SAM alignment record pairs processed.
1600000 SAM alignment record pairs processed.
1700000 SAM alignment record pairs processed.
1800000 SAM alignment record pairs processed.
1900000 SAM alignment record pairs processed.
2000000 SAM alignment record pairs processed.
2100000 SAM alignment record pairs processed.
2200000 SAM alignment record pairs processed.
2300000 SAM alignment record pairs processed.
2400000 SAM alignment record pairs processed.
2500000 SAM alignment record pairs processed.
2600000 SAM alignment record pairs processed.
2700000 SAM alignment record pairs processed.
2800000 SAM alignment record pairs processed.
2900000 SAM alignment record pairs processed.
3000000 SAM alignment record pairs processed.
3100000 SAM alignment record pairs processed.
3200000 SAM alignment record pairs processed.
3300000 SAM alignment record pairs processed.
3400000 SAM alignment record pairs processed.
3500000 SAM alignment record pairs processed.
3600000 SAM alignment record pairs processed.
3700000 SAM alignment record pairs processed.
3800000 SAM alignment record pairs processed.
3900000 SAM alignment record pairs processed.
4000000 SAM alignment record pairs processed.
4100000 SAM alignment record pairs processed.
4112565 SAM alignment pairs processed.
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

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    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
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Attaching package: ‘S4Vectors’

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Loading required package: IRanges
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Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

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Loading required package: BiocParallel

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estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
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Warning message:
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[1] "fold_change"    "id"             "pvalue"         "padj"          
[5] "log2FoldChange" "gff_annotation"
Warning message:
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Warning message:
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Attaching package: ‘plyr’

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