BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716414.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 = 994,065 number of mapped reads = 822,344 (82.73%) number of supplementary alignments = 4,247 (0.43%) number of secondary alignments = 0 number of mapped bases = 48,147,212 bp number of sequenced bases = 48,133,378 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,079 duplication rate = 1.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7723 >>>>>>> ACTG content number of A's = 12,176,644 bp (25.3%) number of C's = 8,546,700 bp (17.76%) number of T's = 15,081,314 bp (31.33%) number of G's = 12,328,019 bp (25.61%) number of N's = 701 bp (0%) GC percentage = 43.37% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 234,084 number of insertions = 3,254 mapped reads with insertion percentage = 0.39% number of deletions = 8,635 mapped reads with deletion percentage = 1.04% homopolymer indels = 42.68% >>>>>>> Coverage mean coverageData = 0.0156X std coverageData = 0.1655X There is a 1.45% of reference with a coverageData >= 1X There is a 0.07% 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 5929479 0.02378922458131007 0.27567453022913696 chr2 243199373 4214104 0.01732777493632765 0.19042148190400138 chr3 198022430 3394916 0.01714409827209978 0.1389590184288534 chr4 191154276 2284554 0.011951362259874322 0.1196295757605064 chr5 180915260 2182880 0.012065759405812422 0.1166647356602849 chr6 171115067 3252246 0.0190061930665638 0.17422720146084353 chr7 159138663 2839067 0.017840208950354194 0.19531831555714027 chr8 146364022 3540084 0.024186845589690066 0.17269679724579873 chr9 141213431 2087815 0.014784818874629567 0.15441391603723342 chr10 135534747 2524984 0.018629790927340573 0.18986847138483343 chr11 135006516 1645387 0.012187463603608584 0.14237735034799157 chr12 133851895 2179115 0.016280045941822488 0.13598371697479636 chr13 115169878 1101570 0.009564740530505728 0.10258885422852813 chr14 107349540 1104567 0.010289443252388413 0.11970491223672203 chr15 102531392 1473605 0.01437223245735316 0.12609406318263638 chr16 90354753 1026053 0.011355827623146731 0.12075430815512775 chr17 81195210 1157892 0.01426059492918363 0.13015132095993995 chr18 78077248 953506 0.01221234129563583 0.22904941357134415 chr19 59128983 1113030 0.018823763635508493 0.20574962863867852 chr20 63025520 875769 0.013895466471359539 0.12447143342653628 chr21 48129895 448953 0.009327944721259002 0.1082272695100235 chr22 51304566 618207 0.012049746215570754 0.11523201313739166 chrMT 16571 2527 0.15249532315490918 0.4242761096134148 chrX 155270560 2087713 0.013445646103163407 0.13273910993537041 chrY 59373566 109189 0.0018390170467443374 0.05674926627074377