BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008831.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,762,421 number of mapped reads = 1,602,178 (90.91%) number of supplementary alignments = 6,957 (0.39%) number of secondary alignments = 0 number of mapped bases = 105,764,446 bp number of sequenced bases = 105,705,530 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,778 duplication rate = 2.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.64 >>>>>>> ACTG content number of A's = 28,959,113 bp (27.4%) number of C's = 19,915,718 bp (18.84%) number of T's = 32,649,296 bp (30.89%) number of G's = 24,028,677 bp (22.73%) number of N's = 152,726 bp (0.14%) GC percentage = 41.57% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 940,239 number of insertions = 7,959 mapped reads with insertion percentage = 0.49% number of deletions = 33,228 mapped reads with deletion percentage = 2.05% homopolymer indels = 44.8% >>>>>>> Coverage mean coverageData = 0.0342X std coverageData = 0.4212X There is a 3% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9189689 0.036869272233428056 0.7496769185030037 chr2 243199373 9811599 0.040343849899645914 0.4372849384700338 chr3 198022430 8464910 0.042747228180161204 0.29663448263700565 chr4 191154276 5621863 0.029410082356724262 0.21666963515660606 chr5 180915260 4520847 0.02498875440358099 0.17391147394814208 chr6 171115067 5654294 0.03304381139037862 0.23105663931961748 chr7 159138663 5345297 0.03358892741231589 0.45770221872948946 chr8 146364022 9474008 0.06472907665792349 0.4258677520795805 chr9 141213431 2955193 0.020927138297489562 0.2956057355749734 chr10 135534747 6335279 0.04674284004824239 1.0276116722491797 chr11 135006516 4526726 0.033529685337558075 0.3207196651671794 chr12 133851895 4657465 0.03479565978501836 0.20472292431389874 chr13 115169878 2653162 0.02303694373975112 0.16365018335512876 chr14 107349540 3525495 0.032841267880607594 0.20604790408858578 chr15 102531392 2434149 0.02374052426792372 0.1689113286464976 chr16 90354753 3029265 0.03352634918940014 0.32913093275181987 chr17 81195210 2943903 0.03625710186598446 0.2880978951699614 chr18 78077248 1460700 0.018708395049989467 0.5800198341031525 chr19 59128983 2327919 0.03937018500724086 0.4961390610688231 chr20 63025520 2286874 0.03628488904177229 0.21416634395282277 chr21 48129895 1047101 0.02175572998860687 0.18726738592084835 chr22 51304566 1301101 0.025360335374438214 0.17440771376538727 chrMT 16571 68839 4.154185022026431 3.3033038584262204 chrX 155270560 5770421 0.03716365162848643 0.24151838989212943 chrY 59373566 358347 0.006035463660713928 0.2240060922001248