BamQC report ----------------------------------- >>>>>>> Input bam file = /Users/strigg/Desktop/20200429/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Users/strigg/Desktop/20200429/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats/genome_results.txt >>>>>>> Reference number of bases = 506,970,227 bp number of contigs = 21 >>>>>>> Globals number of windows = 420 number of reads = 52,851,202 number of mapped reads = 52,851,202 (100%) number of mapped paired reads (first in pair) = 26,425,601 number of mapped paired reads (second in pair) = 26,425,601 number of mapped paired reads (both in pair) = 52,851,202 number of mapped paired reads (singletons) = 0 number of mapped bases = 5,423,561,703 bp number of sequenced bases = 5,401,721,066 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,598,716 duplication rate = 51.98% >>>>>>> Insert size mean insert size = 128.0821 std insert size = 67.8072 median insert size = 115 >>>>>>> Mapping quality mean mapping quality = 18.3105 >>>>>>> ACTG content number of A's = 2,115,706,099 bp (39.17%) number of C's = 583,259,551 bp (10.8%) number of T's = 2,115,926,575 bp (39.17%) number of G's = 586,828,841 bp (10.86%) number of N's = 37,214 bp (0%) GC percentage = 21.66% >>>>>>> Mismatches and indels general error rate = 0.2229 number of mismatches = 1,150,228,632 number of insertions = 31,916,330 mapped reads with insertion percentage = 39.94% number of deletions = 13,183,016 mapped reads with deletion percentage = 20.88% homopolymer indels = 56.21% >>>>>>> Coverage mean coverageData = 10.698X std coverageData = 39.3661X There is a 73.52% of reference with a coverageData >= 1X There is a 67.29% of reference with a coverageData >= 2X There is a 57.22% of reference with a coverageData >= 3X There is a 52.44% of reference with a coverageData >= 4X There is a 46.52% of reference with a coverageData >= 5X There is a 42.9% of reference with a coverageData >= 6X There is a 38.88% of reference with a coverageData >= 7X There is a 36.06% of reference with a coverageData >= 8X There is a 33.1% of reference with a coverageData >= 9X There is a 30.85% of reference with a coverageData >= 10X There is a 28.55% of reference with a coverageData >= 11X There is a 26.72% of reference with a coverageData >= 12X There is a 24.88% of reference with a coverageData >= 13X There is a 23.35% of reference with a coverageData >= 14X There is a 21.85% of reference with a coverageData >= 15X There is a 20.56% of reference with a coverageData >= 16X There is a 19.3% of reference with a coverageData >= 17X There is a 18.21% of reference with a coverageData >= 18X There is a 17.14% of reference with a coverageData >= 19X There is a 16.2% of reference with a coverageData >= 20X There is a 15.28% of reference with a coverageData >= 21X There is a 14.46% of reference with a coverageData >= 22X There is a 13.67% of reference with a coverageData >= 23X There is a 12.95% of reference with a coverageData >= 24X There is a 12.26% of reference with a coverageData >= 25X There is a 11.63% of reference with a coverageData >= 26X There is a 11.02% of reference with a coverageData >= 27X There is a 10.46% of reference with a coverageData >= 28X There is a 9.92% of reference with a coverageData >= 29X There is a 9.43% of reference with a coverageData >= 30X There is a 8.95% of reference with a coverageData >= 31X There is a 8.5% of reference with a coverageData >= 32X There is a 8.08% of reference with a coverageData >= 33X There is a 7.68% of reference with a coverageData >= 34X There is a 7.3% of reference with a coverageData >= 35X There is a 6.94% of reference with a coverageData >= 36X There is a 6.6% of reference with a coverageData >= 37X There is a 6.27% of reference with a coverageData >= 38X There is a 5.97% of reference with a coverageData >= 39X There is a 5.68% of reference with a coverageData >= 40X There is a 5.4% of reference with a coverageData >= 41X There is a 5.14% of reference with a coverageData >= 42X There is a 4.89% of reference with a coverageData >= 43X There is a 4.66% of reference with a coverageData >= 44X There is a 4.43% of reference with a coverageData >= 45X There is a 4.22% of reference with a coverageData >= 46X There is a 4.02% of reference with a coverageData >= 47X There is a 3.83% of reference with a coverageData >= 48X There is a 3.65% of reference with a coverageData >= 49X There is a 3.48% of reference with a coverageData >= 50X There is a 3.32% of reference with a coverageData >= 51X >>>>>>> Coverage per contig Cr_scaffold0000001 36897007 404936863 10.974788903609445 33.09640988628009 Cr_scaffold0000002 35124817 362600191 10.323190893777468 31.37447455780035 Cr_scaffold0000003 33138466 352323453 10.63185764241471 30.839679221729735 Cr_scaffold0000004 31456035 352846366 11.217127842081814 30.673768494685973 Cr_scaffold0000005 30612693 315959864 10.32120447554222 23.56137310862495 Cr_scaffold0000006 30259679 321335601 10.619266681579802 23.217099416471633 Cr_scaffold0000007 29872177 306410488 10.257387267088033 24.058230192792273 Cr_scaffold0000008 27803016 297609720 10.704224318685426 66.78054087946816 Cr_scaffold0000009 25126635 262593429 10.45079967930445 27.248230284130216 Cr_scaffold0000010 24815513 261394168 10.533498461224639 24.95932041974322 Cr_scaffold0000011 35794548 414241160 11.572744541990026 22.83886796469628 Cr_scaffold0000012 22957860 222970252 9.71215313622437 17.7136878229322 Cr_scaffold0000013 21502856 213757476 9.940887666270937 18.651172285298113 Cr_scaffold0000014 21148584 225352401 10.655673259259343 35.4430891315168 Cr_scaffold0000015 19091682 209103661 10.95260548546744 54.8610874266432 Cr_scaffold0000016 18525937 196801680 10.623035153363633 73.44934649894199 Cr_scaffold0000017 17562062 198184660 11.28481723843134 92.4513829670935 Cr_scaffold0000018 14680182 149310118 10.17086286804891 31.10059292544381 Cr_scaffold0000019 14290452 175609581 12.288595280261255 57.10955957751832 Cr_scaffold0000020 8286978 86196812 10.401477112645889 30.02254512609963 Cr_scaffold0000021 8023048 94023759 11.71920684009369 24.918715995775703