BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525056.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 = 1,536,638 number of mapped reads = 1,402,040 (91.24%) number of supplementary alignments = 4,709 (0.31%) number of secondary alignments = 0 number of mapped bases = 80,407,266 bp number of sequenced bases = 80,380,937 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,110 duplication rate = 2.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1508 >>>>>>> ACTG content number of A's = 20,094,228 bp (25%) number of C's = 14,635,421 bp (18.21%) number of T's = 26,330,096 bp (32.76%) number of G's = 19,319,727 bp (24.04%) number of N's = 1,465 bp (0%) GC percentage = 42.24% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 416,479 number of insertions = 6,456 mapped reads with insertion percentage = 0.46% number of deletions = 16,552 mapped reads with deletion percentage = 1.17% homopolymer indels = 41.36% >>>>>>> Coverage mean coverageData = 0.026X std coverageData = 0.2492X There is a 2.37% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% 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 6785965 0.027225468778270367 0.37410623969029416 chr2 243199373 6375121 0.02621355853577797 0.3802569375006337 chr3 198022430 4662503 0.023545327668183853 0.16777137878486578 chr4 191154276 5039370 0.026362842126534485 0.20016544777352563 chr5 180915260 4600599 0.025429579572226246 0.17109752721371055 chr6 171115067 4322437 0.025260411463357578 0.19847706176844881 chr7 159138663 4598843 0.028898338802808718 0.32563355122558896 chr8 146364022 4299938 0.02937838097944589 0.30370369918004403 chr9 141213431 2653843 0.018793134485911613 0.17591873353871965 chr10 135534747 3554752 0.026227606415939967 0.2573430291223279 chr11 135006516 2892106 0.02142197344015603 0.19540998546742608 chr12 133851895 4000365 0.029886502540737284 0.18747480422526921 chr13 115169878 2457506 0.02133809675477819 0.15751898310244752 chr14 107349540 2729642 0.025427607794127484 0.17425789913975584 chr15 102531392 2985315 0.029116107191834478 0.19242999321376963 chr16 90354753 2738137 0.030304294008750152 0.1989962214514554 chr17 81195210 3475844 0.04280848587004086 0.23399856605291378 chr18 78077248 1516180 0.019418973373651695 0.2871516484338722 chr19 59128983 1942007 0.03284357182331379 0.3069125180455406 chr20 63025520 2315679 0.03674192612770192 0.2126739763662606 chr21 48129895 1029142 0.021382593915901957 0.18508686426927753 chr22 51304566 723458 0.014101240033879246 0.12924555663526746 chrMT 16571 17082 1.0308370044052864 1.2268338660094416 chrX 155270560 4404105 0.028364069788889792 0.195941793185182 chrY 59373566 287327 0.004839308455887591 0.1832962833953873