BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008759.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 = 2,001,197 number of mapped reads = 1,788,372 (89.37%) number of supplementary alignments = 14,853 (0.74%) number of secondary alignments = 0 number of mapped bases = 118,589,536 bp number of sequenced bases = 118,528,583 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,288 duplication rate = 4.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.738 >>>>>>> ACTG content number of A's = 32,225,808 bp (27.19%) number of C's = 22,800,910 bp (19.24%) number of T's = 36,635,348 bp (30.91%) number of G's = 26,697,456 bp (22.52%) number of N's = 169,061 bp (0.14%) GC percentage = 41.76% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,022,138 number of insertions = 9,019 mapped reads with insertion percentage = 0.5% number of deletions = 34,149 mapped reads with deletion percentage = 1.89% homopolymer indels = 44.63% >>>>>>> Coverage mean coverageData = 0.0383X std coverageData = 0.4094X There is a 2.92% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% 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 9610563 0.038557829711485456 0.7463991372142239 chr2 243199373 9741872 0.04005714274600535 0.4578217950552873 chr3 198022430 7102370 0.035866492497844814 0.25021959154588463 chr4 191154276 7801837 0.040814347255302835 0.2847807244338274 chr5 180915260 7296078 0.04032870416790712 0.2514156907221018 chr6 171115067 6689418 0.039093097511980056 0.27145190749315906 chr7 159138663 5958361 0.037441316193538715 0.43929126454066425 chr8 146364022 6595484 0.04506219431439237 0.6590139078449792 chr9 141213431 5106766 0.03616345813451696 0.34343124781033446 chr10 135534747 6029247 0.044484880323715066 0.5354703983053313 chr11 135006516 5377699 0.039832884806834064 0.33965548544358687 chr12 133851895 5155844 0.03851902134071393 0.2499273493913707 chr13 115169878 3795959 0.032959651133779966 0.22641491075824124 chr14 107349540 3584456 0.03339051103525921 0.25803272336590743 chr15 102531392 3004279 0.029301065180115764 0.21308179301941982 chr16 90354753 3786566 0.041907767707582574 0.3271927078997011 chr17 81195210 3256870 0.04011160264256968 0.27711564700380165 chr18 78077248 3004731 0.038484079254432736 0.5642920362858466 chr19 59128983 3032322 0.05128317529154865 0.5417769059375 chr20 63025520 2341333 0.03714896759281002 0.2503962574989811 chr21 48129895 1682525 0.03495800271328246 0.2602587695114549 chr22 51304566 1475721 0.028763931069994822 0.2100246571394265 chrMT 16571 189576 11.44022690241989 6.6639216624095265 chrX 155270560 6559239 0.04224393214013011 0.2752063562421481 chrY 59373566 410420 0.006912503789986271 0.23531434921797192