BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237279.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,573,920 number of mapped reads = 2,126,446 (82.62%) number of supplementary alignments = 21,152 (0.82%) number of secondary alignments = 0 number of mapped bases = 141,617,904 bp number of sequenced bases = 141,561,554 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 184,708 duplication rate = 6.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.463 >>>>>>> ACTG content number of A's = 39,750,501 bp (28.08%) number of C's = 25,526,663 bp (18.03%) number of T's = 45,667,943 bp (32.26%) number of G's = 30,614,227 bp (21.63%) number of N's = 2,220 bp (0%) GC percentage = 39.66% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,036,512 number of insertions = 9,941 mapped reads with insertion percentage = 0.46% number of deletions = 32,421 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.82% >>>>>>> Coverage mean coverageData = 0.0457X std coverageData = 0.4501X There is a 3.04% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9420329 0.03779460593600688 0.5120169459871864 chr2 243199373 7639415 0.031412149241026206 0.40433831183103697 chr3 198022430 12628443 0.06377279078940704 0.353420888247168 chr4 191154276 5355692 0.028017641624715733 0.2776812986149218 chr5 180915260 7251440 0.04008196986810289 0.2818543866028301 chr6 171115067 14801042 0.08649759638056888 0.6084902929705959 chr7 159138663 12868007 0.08086034378710345 1.0005210916748348 chr8 146364022 8755564 0.05982046598856104 0.44783918840112996 chr9 141213431 7704080 0.054556283672478716 0.4378152336803234 chr10 135534747 4926315 0.03634724754383464 0.45301636889997415 chr11 135006516 4148643 0.030729205692560796 0.27497216533314806 chr12 133851895 6541621 0.048872083581633266 0.32226752667488623 chr13 115169878 4590300 0.03985677574478285 0.28094076760509334 chr14 107349540 4912913 0.04576557104948936 0.3292728118958804 chr15 102531392 1673446 0.016321303820784956 0.17928790134175093 chr16 90354753 1823409 0.0201805543090799 0.23619238248014857 chr17 81195210 2243245 0.02762779971872725 0.23329911399305323 chr18 78077248 1991942 0.02551245146345322 0.6657533238306216 chr19 59128983 1090028 0.01843474967259288 0.400236611712924 chr20 63025520 2631665 0.0417555460073951 0.2980291683286232 chr21 48129895 666369 0.013845220314733701 0.22432990169857125 chr22 51304566 411291 0.008016654891886231 0.1180133229487355 chrMT 16571 95127 5.740570876833021 4.190758616491757 chrX 155270560 17092361 0.1100811448094217 0.5468392807320749 chrY 59373566 355217 0.005982746598039943 0.16990727476159953