BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524492.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 = 2,090,059 number of mapped reads = 1,864,553 (89.21%) number of supplementary alignments = 4,552 (0.22%) number of secondary alignments = 0 number of mapped bases = 107,259,815 bp number of sequenced bases = 107,223,047 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 147,420 duplication rate = 6.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9559 >>>>>>> ACTG content number of A's = 26,019,223 bp (24.27%) number of C's = 21,520,243 bp (20.07%) number of T's = 34,731,103 bp (32.39%) number of G's = 24,950,432 bp (23.27%) number of N's = 2,046 bp (0%) GC percentage = 43.34% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 520,818 number of insertions = 8,188 mapped reads with insertion percentage = 0.44% number of deletions = 21,788 mapped reads with deletion percentage = 1.16% homopolymer indels = 42.17% >>>>>>> Coverage mean coverageData = 0.0346X std coverageData = 0.3282X There is a 2.8% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 10704241 0.042945694406113434 0.5795399907613136 chr2 243199373 8671892 0.03565754258749672 0.4001875467463716 chr3 198022430 5967109 0.030133500533247672 0.21016173208702021 chr4 191154276 4667863 0.02441934911254614 0.22792582475440756 chr5 180915260 5976792 0.03303641716016659 0.21864482442010613 chr6 171115067 4707587 0.027511236050300585 0.2573979406420387 chr7 159138663 5411899 0.034007442930446136 0.42495300103114714 chr8 146364022 9412815 0.06431098893961797 0.36267642319787335 chr9 141213431 4620651 0.03272104478503889 0.2934486954820668 chr10 135534747 5748587 0.042414119827146615 0.32550938490980763 chr11 135006516 3819736 0.028292975133140982 0.3204712774732292 chr12 133851895 5075057 0.037915466194931344 0.23690958768267562 chr13 115169878 2455580 0.02132137363208807 0.1781578076819988 chr14 107349540 2608417 0.024298352838773227 0.19347643184794844 chr15 102531392 2910831 0.028389656506370264 0.21644804790918185 chr16 90354753 3442284 0.038097431354828674 0.24991402379951705 chr17 81195210 3786890 0.046639327615508354 0.2765211102499105 chr18 78077248 2623318 0.03359900697319659 0.4922318291397407 chr19 59128983 2201139 0.03722605883480188 0.41536069542496074 chr20 63025520 3082808 0.04891364640862939 0.27201520342240215 chr21 48129895 1516039 0.03149890520226566 0.23298360184114403 chr22 51304566 895281 0.01745031816466394 0.15856336512479582 chrMT 16571 14414 0.8698328405044958 1.1114424922378485 chrX 155270560 6593023 0.04246151363143148 0.2811546678134359 chrY 59373566 345562 0.005820132144328336 0.1613079049658714