BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432728.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP127755/SRP127755.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 432,803,854 number of mapped reads = 432,627,531 (99.96%) number of supplementary alignments = 187,764 (0.04%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 216,319,213 number of mapped paired reads (second in pair) = 216,308,318 number of mapped paired reads (both in pair) = 432,564,652 number of mapped paired reads (singletons) = 62,879 number of mapped bases = 59,382,855,021 bp number of sequenced bases = 59,325,416,327 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 215,322,073 duplication rate = 33% >>>>>>> Insert size mean insert size = 52,994.004 std insert size = 2,326,169.8383 median insert size = 307 >>>>>>> Mapping quality mean mapping quality = 55.44 >>>>>>> ACTG content number of A's = 16,274,162,151 bp (27.43%) number of C's = 12,783,654,048 bp (21.55%) number of T's = 16,055,035,745 bp (27.06%) number of G's = 14,212,262,602 bp (23.96%) number of N's = 301,781 bp (0%) GC percentage = 45.5% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 562,154,040 number of insertions = 12,091,914 mapped reads with insertion percentage = 2.73% number of deletions = 39,408,925 mapped reads with deletion percentage = 8.7% homopolymer indels = 51.56% >>>>>>> Coverage mean coverageData = 19.1824X std coverageData = 54.0749X There is a 64.82% of reference with a coverageData >= 1X There is a 56.35% of reference with a coverageData >= 2X There is a 50.55% of reference with a coverageData >= 3X There is a 46.14% of reference with a coverageData >= 4X There is a 42.6% of reference with a coverageData >= 5X There is a 39.65% of reference with a coverageData >= 6X There is a 37.14% of reference with a coverageData >= 7X There is a 34.96% of reference with a coverageData >= 8X There is a 33.05% of reference with a coverageData >= 9X There is a 31.35% of reference with a coverageData >= 10X There is a 29.83% of reference with a coverageData >= 11X There is a 28.46% of reference with a coverageData >= 12X There is a 27.21% of reference with a coverageData >= 13X There is a 26.07% of reference with a coverageData >= 14X There is a 25.02% of reference with a coverageData >= 15X There is a 24.05% of reference with a coverageData >= 16X There is a 23.15% of reference with a coverageData >= 17X There is a 22.31% of reference with a coverageData >= 18X There is a 21.53% of reference with a coverageData >= 19X There is a 20.8% of reference with a coverageData >= 20X There is a 20.12% of reference with a coverageData >= 21X There is a 19.48% of reference with a coverageData >= 22X There is a 18.87% of reference with a coverageData >= 23X There is a 18.3% of reference with a coverageData >= 24X There is a 17.76% of reference with a coverageData >= 25X There is a 17.25% of reference with a coverageData >= 26X There is a 16.76% of reference with a coverageData >= 27X There is a 16.3% of reference with a coverageData >= 28X There is a 15.86% of reference with a coverageData >= 29X There is a 15.44% of reference with a coverageData >= 30X There is a 15.04% of reference with a coverageData >= 31X There is a 14.66% of reference with a coverageData >= 32X There is a 14.29% of reference with a coverageData >= 33X There is a 13.94% of reference with a coverageData >= 34X There is a 13.6% of reference with a coverageData >= 35X There is a 13.28% of reference with a coverageData >= 36X There is a 12.97% of reference with a coverageData >= 37X There is a 12.68% of reference with a coverageData >= 38X There is a 12.39% of reference with a coverageData >= 39X There is a 12.12% of reference with a coverageData >= 40X There is a 11.85% of reference with a coverageData >= 41X There is a 11.59% of reference with a coverageData >= 42X There is a 11.35% of reference with a coverageData >= 43X There is a 11.11% of reference with a coverageData >= 44X There is a 10.88% of reference with a coverageData >= 45X There is a 10.66% of reference with a coverageData >= 46X There is a 10.44% of reference with a coverageData >= 47X There is a 10.24% of reference with a coverageData >= 48X There is a 10.04% of reference with a coverageData >= 49X There is a 9.84% of reference with a coverageData >= 50X There is a 9.65% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5455865631 21.889075377669773 60.671887768688634 chr2 243199373 5303246502 21.80616848054127 62.07114558095803 chr3 198022430 3754802692 18.96150194702691 49.36075670598289 chr4 191154276 2946595400 15.414750125704748 44.09841605763438 chr5 180915260 3456342781 19.1047608753402 51.421791059399986 chr6 171115067 3138304968 18.340319312734746 49.66858102906781 chr7 159138663 2928847321 18.40437305295194 48.942923339713566 chr8 146364022 2909112170 19.875869289790355 52.12992772713101 chr9 141213431 2385665086 16.894038117379925 54.238793671534665 chr10 135534747 2921864961 21.558050800065313 55.83774120375693 chr11 135006516 2996358881 22.19417973129534 56.90613962520195 chr12 133851895 3204365813 23.93963726101898 62.22139669738995 chr13 115169878 1587485148 13.783857164457533 41.791458385215286 chr14 107349540 1784837486 16.626410192349216 47.72438644149872 chr15 102531392 1994515391 19.45272908223074 55.36327282418389 chr16 90354753 2063085832 22.833174387627402 65.1595185105607 chr17 81195210 2139120340 26.345400670803116 66.60469893418515 chr18 78077248 1424354475 18.242887800041313 51.82505467411221 chr19 59128983 1443986980 24.420967632742812 65.1864871633271 chr20 63025520 1855651709 29.44286233576494 71.10111020141515 chr21 48129895 723906579 15.040684776062777 53.28696515824471 chr22 51304566 1146446095 22.34588818079077 64.50008884714468 chrMT 16571 5465542 329.8257196306801 611.7482519050377 chrX 155270560 1635009721 10.530069067825865 30.12457139587535 chrY 59373566 177617517 2.9915251679510035 22.460472362953904