BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238296.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 = 1,898,228 number of mapped reads = 1,541,524 (81.21%) number of supplementary alignments = 19,540 (1.03%) number of secondary alignments = 0 number of mapped bases = 98,179,507 bp number of sequenced bases = 98,125,110 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 131,506 duplication rate = 6.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6355 >>>>>>> ACTG content number of A's = 26,620,179 bp (27.13%) number of C's = 18,507,238 bp (18.86%) number of T's = 30,580,182 bp (31.16%) number of G's = 22,395,995 bp (22.82%) number of N's = 21,516 bp (0.02%) GC percentage = 41.68% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 895,420 number of insertions = 7,800 mapped reads with insertion percentage = 0.5% number of deletions = 32,375 mapped reads with deletion percentage = 2.07% homopolymer indels = 43.88% >>>>>>> Coverage mean coverageData = 0.0317X std coverageData = 0.3264X There is a 2.17% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% 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 8450491 0.0339035905551465 0.5395920312977044 chr2 243199373 7719665 0.031742125420693414 0.3893793300779801 chr3 198022430 7931969 0.04005591184796591 0.27576450200186264 chr4 191154276 3560444 0.018626023306954433 0.23184159256907957 chr5 180915260 6060796 0.03350074504494535 0.2536071148691027 chr6 171115067 7642580 0.044663396005916886 0.32913325085292433 chr7 159138663 5281422 0.03318754789337397 0.36491911674191874 chr8 146364022 3639625 0.024866937586615376 0.35558722471497256 chr9 141213431 4295010 0.030415024757807916 0.28422290679410545 chr10 135534747 4795611 0.03538288967330274 0.35382004472812734 chr11 135006516 3040411 0.02252047597465592 0.2309268425650468 chr12 133851895 4714196 0.03521949390406464 0.2637950284026876 chr13 115169878 3497030 0.030364102669276076 0.24224813068103934 chr14 107349540 3800082 0.03539914563210984 0.2782660346396967 chr15 102531392 2832150 0.02762227201596951 0.24625073151256616 chr16 90354753 2230529 0.024686349372235017 0.23359683262531322 chr17 81195210 2045691 0.025194725156816516 0.22828816270032112 chr18 78077248 2067290 0.026477495723209916 0.41682184295204455 chr19 59128983 2656306 0.044923925040280165 0.41659364323845477 chr20 63025520 2129788 0.033792470097827036 0.263426072594102 chr21 48129895 1599410 0.033231113427527735 0.27133120918346837 chr22 51304566 1106541 0.021568080314722866 0.20308370412924576 chrMT 16571 9352 0.5643594230885282 1.1538106755138575 chrX 155270560 6753192 0.04349306140198116 0.2996193375201056 chrY 59373566 319926 0.00538835750576275 0.17232018225950246