BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013307.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 = 1,732,854 number of mapped reads = 1,545,344 (89.18%) number of supplementary alignments = 9,337 (0.54%) number of secondary alignments = 0 number of mapped bases = 102,379,840 bp number of sequenced bases = 102,337,429 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,230 duplication rate = 3.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6144 >>>>>>> ACTG content number of A's = 27,647,370 bp (27.02%) number of C's = 19,324,004 bp (18.88%) number of T's = 31,923,270 bp (31.19%) number of G's = 23,417,638 bp (22.88%) number of N's = 25,147 bp (0.02%) GC percentage = 41.77% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 795,818 number of insertions = 6,784 mapped reads with insertion percentage = 0.44% number of deletions = 24,605 mapped reads with deletion percentage = 1.58% homopolymer indels = 45.95% >>>>>>> Coverage mean coverageData = 0.0331X std coverageData = 0.2787X There is a 2.76% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 7583769 0.030426279258899017 0.3714907613389902 chr2 243199373 10227458 0.04205380085416585 0.37104297256245683 chr3 198022430 6569573 0.03317590335599861 0.21150141318931676 chr4 191154276 6391035 0.03343391073292025 0.214163512987992 chr5 180915260 5549085 0.030672288230412403 0.20285630699324067 chr6 171115067 5561823 0.03250340894878649 0.2448604004136045 chr7 159138663 6319583 0.03971117314212951 0.4646308526045836 chr8 146364022 5549460 0.037915465318382684 0.2843013127140471 chr9 141213431 3702368 0.026218242654269905 0.22461193080547087 chr10 135534747 4844385 0.035742753111126555 0.281932872111041 chr11 135006516 4257522 0.03153567787794776 0.2258216982247818 chr12 133851895 5137537 0.038382250770525136 0.23059233199738002 chr13 115169878 2620658 0.02275471716658413 0.1795803945565576 chr14 107349540 3357163 0.03127319409100402 0.21260460632406805 chr15 102531392 2921437 0.02849309799675791 0.19754116974435063 chr16 90354753 3347770 0.03705139894522206 0.2335614834335948 chr17 81195210 2749767 0.03386612338338678 0.224626006746814 chr18 78077248 2568106 0.03289186114756504 0.363131784196098 chr19 59128983 2073317 0.03506431017086832 0.3090392593743726 chr20 63025520 2330035 0.03696970687429473 0.22652922716010834 chr21 48129895 1698595 0.03529189083001324 0.22457334145845312 chr22 51304566 1076082 0.020974390466532745 0.1680861660969054 chrMT 16571 250782 15.133787942791624 11.784420336021881 chrX 155270560 5485947 0.03533153355021068 0.2273501609147276 chrY 59373566 206583 0.003479376664019136 0.07694142946877076