BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525020.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 = 986,864 number of mapped reads = 905,343 (91.74%) number of supplementary alignments = 3,363 (0.34%) number of secondary alignments = 0 number of mapped bases = 52,868,760 bp number of sequenced bases = 52,851,859 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,392 duplication rate = 1.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8082 >>>>>>> ACTG content number of A's = 13,198,512 bp (24.97%) number of C's = 9,932,082 bp (18.79%) number of T's = 15,980,696 bp (30.24%) number of G's = 13,740,082 bp (26%) number of N's = 487 bp (0%) GC percentage = 44.79% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 258,913 number of insertions = 2,929 mapped reads with insertion percentage = 0.32% number of deletions = 10,168 mapped reads with deletion percentage = 1.11% homopolymer indels = 45.31% >>>>>>> Coverage mean coverageData = 0.0171X std coverageData = 0.1757X There is a 1.6% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5470410 0.021947427765887092 0.30862132396073594 chr2 243199373 4167938 0.017137947144296298 0.19722858688808123 chr3 198022430 3002487 0.015162358122764173 0.12920994072379954 chr4 191154276 3673566 0.019217807086878872 0.1514507635757561 chr5 180915260 2433732 0.013452331218494228 0.12239403597287692 chr6 171115067 3622712 0.021171204053001363 0.18339018284716885 chr7 159138663 2942745 0.018491703678571184 0.1663312730117637 chr8 146364022 3348143 0.022875450908284006 0.19024465401213608 chr9 141213431 1390349 0.009845727776418095 0.13587284219284468 chr10 135534747 2891488 0.021333924060078852 0.196132018150255 chr11 135006516 2313757 0.017138113541127157 0.16776401112960612 chr12 133851895 3032997 0.02265935047090667 0.15872648704640455 chr13 115169878 1043367 0.009059374014444992 0.09920416460229095 chr14 107349540 1274200 0.011869636330067181 0.1168933002072455 chr15 102531392 1559462 0.015209605268989228 0.13055636493589215 chr16 90354753 1769395 0.01958275509867201 0.15400972694625792 chr17 81195210 1325880 0.016329534710237216 0.16018652555813587 chr18 78077248 1101690 0.014110256550025943 0.2262637954493166 chr19 59128983 1223830 0.02069763317255093 0.2010579303726159 chr20 63025520 1364084 0.021643359705719206 0.15377521419564152 chr21 48129895 771332 0.01602604784406864 0.13588611704187883 chr22 51304566 772874 0.015064429158215665 0.1277723938588559 chrMT 16571 16401 0.9897411139943274 1.1517829268040392 chrX 155270560 2209716 0.014231390677022096 0.13814152610720914 chrY 59373566 146205 0.0024624594722843494 0.07122858552075206