BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438278.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 572,213,834 number of mapped reads = 570,459,742 (99.69%) number of supplementary alignments = 8,929,915 (1.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 285,337,537 number of mapped paired reads (second in pair) = 285,122,205 number of mapped paired reads (both in pair) = 569,211,290 number of mapped paired reads (singletons) = 1,248,452 number of mapped bases = 81,730,992,598 bp number of sequenced bases = 81,708,474,845 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 248,752,162 duplication rate = 40.62% >>>>>>> Insert size mean insert size = 41,077.0937 std insert size = 1,998,954.9707 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 54.9646 >>>>>>> ACTG content number of A's = 24,490,806,544 bp (29.97%) number of C's = 16,522,487,306 bp (20.22%) number of T's = 23,388,751,039 bp (28.62%) number of G's = 17,305,923,254 bp (21.18%) number of N's = 506,702 bp (0%) GC percentage = 41.4% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 413,221,188 number of insertions = 10,290,782 mapped reads with insertion percentage = 1.78% number of deletions = 9,247,238 mapped reads with deletion percentage = 1.6% homopolymer indels = 48.71% >>>>>>> Coverage mean coverageData = 26.4015X std coverageData = 97.4001X There is a 88.04% of reference with a coverageData >= 1X There is a 86.71% of reference with a coverageData >= 2X There is a 85.23% of reference with a coverageData >= 3X There is a 83.73% of reference with a coverageData >= 4X There is a 82.06% of reference with a coverageData >= 5X There is a 80.31% of reference with a coverageData >= 6X There is a 78.43% of reference with a coverageData >= 7X There is a 76.47% of reference with a coverageData >= 8X There is a 74.43% of reference with a coverageData >= 9X There is a 72.33% of reference with a coverageData >= 10X There is a 70.18% of reference with a coverageData >= 11X There is a 68.01% of reference with a coverageData >= 12X There is a 65.83% of reference with a coverageData >= 13X There is a 63.64% of reference with a coverageData >= 14X There is a 61.46% of reference with a coverageData >= 15X There is a 59.29% of reference with a coverageData >= 16X There is a 57.16% of reference with a coverageData >= 17X There is a 55.06% of reference with a coverageData >= 18X There is a 52.99% of reference with a coverageData >= 19X There is a 50.98% of reference with a coverageData >= 20X There is a 49% of reference with a coverageData >= 21X There is a 47.08% of reference with a coverageData >= 22X There is a 45.22% of reference with a coverageData >= 23X There is a 43.4% of reference with a coverageData >= 24X There is a 41.65% of reference with a coverageData >= 25X There is a 39.95% of reference with a coverageData >= 26X There is a 38.31% of reference with a coverageData >= 27X There is a 36.72% of reference with a coverageData >= 28X There is a 35.2% of reference with a coverageData >= 29X There is a 33.73% of reference with a coverageData >= 30X There is a 32.31% of reference with a coverageData >= 31X There is a 30.95% of reference with a coverageData >= 32X There is a 29.64% of reference with a coverageData >= 33X There is a 28.39% of reference with a coverageData >= 34X There is a 27.18% of reference with a coverageData >= 35X There is a 26.03% of reference with a coverageData >= 36X There is a 24.92% of reference with a coverageData >= 37X There is a 23.86% of reference with a coverageData >= 38X There is a 22.84% of reference with a coverageData >= 39X There is a 21.87% of reference with a coverageData >= 40X There is a 20.93% of reference with a coverageData >= 41X There is a 20.04% of reference with a coverageData >= 42X There is a 19.19% of reference with a coverageData >= 43X There is a 18.37% of reference with a coverageData >= 44X There is a 17.59% of reference with a coverageData >= 45X There is a 16.84% of reference with a coverageData >= 46X There is a 16.13% of reference with a coverageData >= 47X There is a 15.44% of reference with a coverageData >= 48X There is a 14.79% of reference with a coverageData >= 49X There is a 14.17% of reference with a coverageData >= 50X There is a 13.57% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7014012800 28.140402506760456 30.105929044382194 chr2 243199373 7331037039 30.144144487576455 130.10803710636796 chr3 198022430 5891327799 29.750810547067825 222.07365909166793 chr4 191154276 4986823872 26.087953543869457 34.89829821416506 chr5 180915260 5051373626 27.92121364444326 49.9573842696068 chr6 171115067 4242696296 24.794405135580494 26.225917976340554 chr7 159138663 4421207776 27.78210959331737 32.40274946536291 chr8 146364022 4064239690 27.768024098162595 26.98316524757467 chr9 141213431 3478477894 24.6327694849366 31.295662725259444 chr10 135534747 3936424814 29.043657815659625 43.865439472288436 chr11 135006516 4064775392 30.107994135631202 29.228603390366427 chr12 133851895 4082610842 30.500956613277683 28.914925918183926 chr13 115169878 2536111354 22.020613358642265 23.407596940380383 chr14 107349540 2626580734 24.467554625758062 31.9922338297266 chr15 102531392 2383505565 23.246593248241474 28.62134061684887 chr16 90354753 2338480708 25.88110343237837 37.234061633732466 chr17 81195210 2502996716 30.82690119281667 33.66667835249303 chr18 78077248 2154126044 27.589676880004788 24.415267571103772 chr19 59128983 1598570361 27.035309587516497 322.50472588010786 chr20 63025520 2011208448 31.911017124491792 31.61241413365733 chr21 48129895 990549043 20.58074390147745 120.490504629172 chr22 51304566 1253203076 24.426735741220384 32.932533064311464 chrMT 16571 288909969 17434.673163961135 6725.252504484901 chrX 155270560 2151822863 13.858537400779646 36.93075143222788 chrY 59373566 329919877 5.556679499425721 15.60166922931714