BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716364.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 = 1,302,060 number of mapped reads = 1,160,894 (89.16%) number of supplementary alignments = 7,282 (0.56%) number of secondary alignments = 0 number of mapped bases = 66,376,133 bp number of sequenced bases = 66,356,526 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,621 duplication rate = 2.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3392 >>>>>>> ACTG content number of A's = 17,212,949 bp (25.94%) number of C's = 12,873,082 bp (19.4%) number of T's = 20,636,341 bp (31.1%) number of G's = 15,633,101 bp (23.56%) number of N's = 1,053 bp (0%) GC percentage = 42.96% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 366,132 number of insertions = 4,722 mapped reads with insertion percentage = 0.4% number of deletions = 11,820 mapped reads with deletion percentage = 1.01% homopolymer indels = 42.61% >>>>>>> Coverage mean coverageData = 0.0214X std coverageData = 0.2309X There is a 1.97% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% 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 4825360 0.019359470322041845 0.39291904106670755 chr2 243199373 5634686 0.023168998877312073 0.2632600773450699 chr3 198022430 4031028 0.020356421239755517 0.15105360744546337 chr4 191154276 4164951 0.021788427060873073 0.1736085491182408 chr5 180915260 3714702 0.02053282846344747 0.15402337306546107 chr6 171115067 3491832 0.020406338618913084 0.16828708825513122 chr7 159138663 4264380 0.026796630809949686 0.30602674764417476 chr8 146364022 2920226 0.019951802089723934 0.20354711279087906 chr9 141213431 2927018 0.020727617615919267 0.24429757734858848 chr10 135534747 2618547 0.019320115748620536 0.23162817331752583 chr11 135006516 2409189 0.0178449831265922 0.19166306283169227 chr12 133851895 4548299 0.03398008672196983 0.20848120295074524 chr13 115169878 2470980 0.02145508915100179 0.15404027368054268 chr14 107349540 2337049 0.021770461242777567 0.1768563022409301 chr15 102531392 1708260 0.01666084861112585 0.1385655980944016 chr16 90354753 1914007 0.021183246441944234 0.1710503305643539 chr17 81195210 1985351 0.02445157787017239 0.1704939891957087 chr18 78077248 2100814 0.026906865364926796 0.42548835945088226 chr19 59128983 1222720 0.02067886065282063 0.3000368354569857 chr20 63025520 1961522 0.031122662692826653 0.19385034493812994 chr21 48129895 800427 0.016630557785343184 0.1539978059195265 chr22 51304566 662340 0.012909962048991896 0.11933206854890549 chrMT 16571 11834 0.7141391587713475 0.9045078330095906 chrX 155270560 3452187 0.022233364779517765 0.1878825207647436 chrY 59373566 198424 0.0033419586083140097 0.08935897601274094