BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751182.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 5,238,140 number of mapped reads = 4,059,552 (77.5%) number of supplementary alignments = 220,874 (4.22%) number of secondary alignments = 0 number of mapped bases = 399,072,519 bp number of sequenced bases = 398,934,770 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 145,526 duplication rate = 1.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.0186 >>>>>>> ACTG content number of A's = 117,547,966 bp (29.47%) number of C's = 81,930,909 bp (20.54%) number of T's = 118,455,325 bp (29.69%) number of G's = 80,997,684 bp (20.3%) number of N's = 2,886 bp (0%) GC percentage = 40.84% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 1,563,558 number of insertions = 234,279 mapped reads with insertion percentage = 5.56% number of deletions = 61,167 mapped reads with deletion percentage = 1.47% homopolymer indels = 51.85% >>>>>>> Coverage mean coverageData = 0.1289X std coverageData = 1.7175X There is a 10.32% of reference with a coverageData >= 1X There is a 1.69% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.1% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 38541117 0.15462796780755061 5.156466634033586 chr2 243199373 29918914 0.12302216749547294 0.6479404320151609 chr3 198022430 25317752 0.12785295079956346 0.45824535031067226 chr4 191154276 21703655 0.11353999216842002 0.4373333177636379 chr5 180915260 34483753 0.19060721024859925 0.5386573974331023 chr6 171115067 20074458 0.11731554884059392 0.8369319260492257 chr7 159138663 23289689 0.1463484018336889 1.013930197705187 chr8 146364022 27380922 0.1870741294605856 1.018564902422579 chr9 141213431 17327582 0.12270491466211879 0.8152518716191894 chr10 135534747 16617565 0.12260741520401407 1.688034463275996 chr11 135006516 17392617 0.12882798190274017 0.6941853608080205 chr12 133851895 17675277 0.132051003088152 0.4298691091187891 chr13 115169878 15205562 0.13202724761069903 0.4194126710490241 chr14 107349540 10166120 0.09470110444814202 0.3908713399775822 chr15 102531392 12414136 0.12107644066706906 0.4024764926642229 chr16 90354753 10468796 0.11586325735404313 0.7032952887274785 chr17 81195210 11364295 0.13996262833731202 0.7578845692493615 chr18 78077248 7461538 0.09556609884610687 1.8365974987946942 chr19 59128983 8014458 0.13554195579518086 3.5518418084404613 chr20 63025520 7360481 0.11678572425899858 0.4134965852155722 chr21 48129895 4109949 0.08539285198939245 0.38425398373742337 chr22 51304566 3660361 0.07134571609084463 0.31173360958495394 chrMT 16571 164042 9.89934222436787 8.181253546850328 chrX 155270560 17776518 0.11448736965977324 0.47435956316240624 chrY 59373566 1182962 0.019924051723623944 0.9129480590506184