BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525052.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 = 641,334 number of mapped reads = 578,380 (90.18%) number of supplementary alignments = 1,697 (0.26%) number of secondary alignments = 0 number of mapped bases = 33,934,873 bp number of sequenced bases = 33,923,349 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,405 duplication rate = 3.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4593 >>>>>>> ACTG content number of A's = 8,872,422 bp (26.15%) number of C's = 6,508,321 bp (19.19%) number of T's = 10,780,960 bp (31.78%) number of G's = 7,758,372 bp (22.87%) number of N's = 3,274 bp (0.01%) GC percentage = 42.06% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 168,225 number of insertions = 2,707 mapped reads with insertion percentage = 0.47% number of deletions = 7,256 mapped reads with deletion percentage = 1.25% homopolymer indels = 41.74% >>>>>>> Coverage mean coverageData = 0.011X std coverageData = 0.138X There is a 1.01% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 2730200 0.01095363369225066 0.2295661541588211 chr2 243199373 2891507 0.011889450882753715 0.15775412252956306 chr3 198022430 2235331 0.011288271737701633 0.11223435187738587 chr4 191154276 2251832 0.011780181155874326 0.12435307550240025 chr5 180915260 2099154 0.011602968152050855 0.1142445982302869 chr6 171115067 1930622 0.011282595003746806 0.11738659515237879 chr7 159138663 1850310 0.01162702994431969 0.1473220708247112 chr8 146364022 1696715 0.01159243218938053 0.14708203981525494 chr9 141213431 1429251 0.010121211487312421 0.1181983060544322 chr10 135534747 1661211 0.012256716722243927 0.14906227221838703 chr11 135006516 1510371 0.011187393355147391 0.12250110815172238 chr12 133851895 1545794 0.011548540272814217 0.11487526541876235 chr13 115169878 1090667 0.009470071679679995 0.10284746124829561 chr14 107349540 1029149 0.009586897158571896 0.10461759353999926 chr15 102531392 989155 0.009647338056231598 0.10403739546857033 chr16 90354753 960708 0.010632622724340799 0.11254914246932707 chr17 81195210 869860 0.01071319354922538 0.11378505336483516 chr18 78077248 905405 0.011596271938273233 0.16288098214746494 chr19 59128983 662372 0.011202154449367072 0.1677443056753444 chr20 63025520 702187 0.01114131228112041 0.11358704728982806 chr21 48129895 452160 0.009394576904853003 0.10981573038149436 chr22 51304566 389785 0.007597471928716832 0.09279200416189586 chrMT 16571 26505 1.5994810210608894 1.4752632828475956 chrX 155270560 1900325 0.012238797876429376 0.12412740950855972 chrY 59373566 124297 0.002093473718590526 0.08760525368206278