BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524748.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 = 1,858,627 number of mapped reads = 1,692,660 (91.07%) number of supplementary alignments = 6,553 (0.35%) number of secondary alignments = 0 number of mapped bases = 97,440,760 bp number of sequenced bases = 97,409,516 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,053 duplication rate = 2.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5202 >>>>>>> ACTG content number of A's = 23,482,480 bp (24.11%) number of C's = 18,175,086 bp (18.66%) number of T's = 31,365,083 bp (32.2%) number of G's = 24,374,940 bp (25.02%) number of N's = 11,927 bp (0.01%) GC percentage = 43.68% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 496,548 number of insertions = 5,702 mapped reads with insertion percentage = 0.34% number of deletions = 19,285 mapped reads with deletion percentage = 1.13% homopolymer indels = 42.45% >>>>>>> Coverage mean coverageData = 0.0315X std coverageData = 0.2675X There is a 2.79% 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% 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 7802661 0.031304479678708606 0.3686308408702313 chr2 243199373 8196945 0.033704630480276776 0.419948300327271 chr3 198022430 6360414 0.032119664423873595 0.20281122494843934 chr4 191154276 6190883 0.032386840250437296 0.2283321118620241 chr5 180915260 5785128 0.031977004040455184 0.19792430331338953 chr6 171115067 5518408 0.03224969078847978 0.21861544532923513 chr7 159138663 5337025 0.033536947586395145 0.319869282950808 chr8 146364022 4819495 0.03292813994958406 0.2429871362042291 chr9 141213431 4169613 0.029527028487821388 0.23951529657305998 chr10 135534747 4786968 0.03531912004823383 0.32672843489918896 chr11 135006516 4415486 0.03270572510737185 0.2361753709049787 chr12 133851895 4392519 0.0328162630794282 0.20246280207027276 chr13 115169878 3002906 0.02607371000254077 0.17859258656174654 chr14 107349540 2923570 0.027234117631058315 0.18879136094915155 chr15 102531392 2830281 0.027604043452370178 0.18550455207392028 chr16 90354753 2963989 0.032803907947155805 0.22557174313206566 chr17 81195210 2801182 0.034499350392714054 0.21462000077348645 chr18 78077248 2544880 0.03259438652345943 0.3565827599525099 chr19 59128983 2163871 0.03659577571290208 0.3123373836528104 chr20 63025520 2135278 0.033879577669490075 0.21312797024948674 chr21 48129895 1280407 0.026603153819471245 0.20861554100969099 chr22 51304566 1239529 0.024160208274639727 0.17422313452275667 chrMT 16571 35067 2.1161667974171747 1.9497431873166828 chrX 155270560 5418324 0.03489601634720709 0.22291227737401426 chrY 59373566 325931 0.0054894967905414335 0.1551202646658402