BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524985.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,165,951 number of mapped reads = 1,077,259 (92.39%) number of supplementary alignments = 2,433 (0.21%) number of secondary alignments = 0 number of mapped bases = 62,622,389 bp number of sequenced bases = 62,603,363 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,513 duplication rate = 2.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6115 >>>>>>> ACTG content number of A's = 15,784,517 bp (25.21%) number of C's = 11,420,586 bp (18.24%) number of T's = 20,266,667 bp (32.37%) number of G's = 15,130,820 bp (24.17%) number of N's = 773 bp (0%) GC percentage = 42.41% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 304,476 number of insertions = 4,077 mapped reads with insertion percentage = 0.38% number of deletions = 11,232 mapped reads with deletion percentage = 1.04% homopolymer indels = 43.12% >>>>>>> Coverage mean coverageData = 0.0202X std coverageData = 0.2092X There is a 1.84% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 4853042 0.01947053122888709 0.3688112347083803 chr2 243199373 5389660 0.022161488056139027 0.23061295220774738 chr3 198022430 4432551 0.02238408547960956 0.16127193486150418 chr4 191154276 4184475 0.021890564456952036 0.18012791238274983 chr5 180915260 3763825 0.02080435337516581 0.1563468033546072 chr6 171115067 3888472 0.02272431100412683 0.19311802067724454 chr7 159138663 3545047 0.022276465901941128 0.24768998458126185 chr8 146364022 3339944 0.02281943304345654 0.2224894945152905 chr9 141213431 2545903 0.018028759601485783 0.1810543377731876 chr10 135534747 3151528 0.023252546448476418 0.21845378092444628 chr11 135006516 2596063 0.019229168168446033 0.1873695266875398 chr12 133851895 2723896 0.020350074236901914 0.15474966779579483 chr13 115169878 2099672 0.018231086430429318 0.1462362471407276 chr14 107349540 1918331 0.017869950816743137 0.148908919740885 chr15 102531392 1865084 0.01819037041845682 0.15065308447541342 chr16 90354753 1586721 0.01756101308804419 0.15220943960510155 chr17 81195210 1450494 0.017864280417527093 0.15685679180056472 chr18 78077248 1759749 0.02253856334690485 0.2855466190636231 chr19 59128983 1065235 0.01801544599540973 0.2556584916592066 chr20 63025520 1099321 0.01744247409620738 0.14519084002701485 chr21 48129895 843036 0.017515849556704828 0.15379250729104554 chr22 51304566 658638 0.012837804728725314 0.12128884906523144 chrMT 16571 1325 0.0799589644559773 0.2920149444518645 chrX 155270560 3667941 0.023622900567886147 0.17903141010572146 chrY 59373566 192436 0.0032411056462399446 0.10553977186159333