BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716407.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 = 2,450,504 number of mapped reads = 2,125,666 (86.74%) number of supplementary alignments = 7,175 (0.29%) number of secondary alignments = 0 number of mapped bases = 120,217,384 bp number of sequenced bases = 120,179,728 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,797 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1552 >>>>>>> ACTG content number of A's = 28,095,619 bp (23.38%) number of C's = 24,804,888 bp (20.64%) number of T's = 38,239,253 bp (31.82%) number of G's = 29,038,311 bp (24.16%) number of N's = 1,657 bp (0%) GC percentage = 44.8% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 631,443 number of insertions = 9,062 mapped reads with insertion percentage = 0.42% number of deletions = 23,613 mapped reads with deletion percentage = 1.1% homopolymer indels = 40.35% >>>>>>> Coverage mean coverageData = 0.0388X std coverageData = 0.3073X There is a 3.39% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.06% 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 0.01% 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 9642071 0.03868424063023698 0.4009691026494988 chr2 243199373 10197689 0.04193139511095697 0.5150025899821999 chr3 198022430 7983332 0.04031529155560812 0.2294307144143762 chr4 191154276 7607424 0.03979729964293344 0.2530242075785572 chr5 180915260 7074316 0.039102925867060635 0.2216991661308137 chr6 171115067 6756819 0.039486990353689896 0.2608419843956786 chr7 159138663 6517632 0.04095567901057457 0.4024929181527637 chr8 146364022 6000668 0.04099824477356874 0.276393128605708 chr9 141213431 4979211 0.035260180032025426 0.2510573218524032 chr10 135534747 5834891 0.04305088642693228 0.33236284758821893 chr11 135006516 5392809 0.03994480533072937 0.27737159892859403 chr12 133851895 5456513 0.04076530257565648 0.2304317156144956 chr13 115169878 3705786 0.0321766946735847 0.20392193493296662 chr14 107349540 3574531 0.033298056051288154 0.21384663454832245 chr15 102531392 3537615 0.03450275014309764 0.21757343175225186 chr16 90354753 3729047 0.041271176957342795 0.24929692231428774 chr17 81195210 3599834 0.044335546394916645 0.2553802614431682 chr18 78077248 3150947 0.04035678870238869 0.4177435472278145 chr19 59128983 2780803 0.04702944070592251 0.3521016581675781 chr20 63025520 2568632 0.04075542732531203 0.23465355604643148 chr21 48129895 1534738 0.031887416334484005 0.22590162785914863 chr22 51304566 1566159 0.030526698150024307 0.1978777086793782 chrMT 16571 16257 0.9810512340836401 1.3254897950174296 chrX 155270560 6648751 0.04282042262229234 0.2591614646302228 chrY 59373566 360909 0.006078614176551228 0.145882833483872