BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525098.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 = 1,938,236 number of mapped reads = 1,787,546 (92.23%) number of supplementary alignments = 6,398 (0.33%) number of secondary alignments = 0 number of mapped bases = 103,979,626 bp number of sequenced bases = 103,945,991 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,296 duplication rate = 2.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2863 >>>>>>> ACTG content number of A's = 26,293,729 bp (25.3%) number of C's = 18,485,768 bp (17.78%) number of T's = 32,729,151 bp (31.49%) number of G's = 26,435,356 bp (25.43%) number of N's = 1,987 bp (0%) GC percentage = 43.22% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 526,931 number of insertions = 7,244 mapped reads with insertion percentage = 0.4% number of deletions = 20,831 mapped reads with deletion percentage = 1.16% homopolymer indels = 41.92% >>>>>>> Coverage mean coverageData = 0.0336X std coverageData = 0.3055X There is a 3.01% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% 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 8679978 0.03482429839161765 0.5015407360679166 chr2 243199373 8335045 0.0342724773389938 0.4239633434547936 chr3 198022430 6075136 0.03067902964325809 0.19616511302018788 chr4 191154276 6532671 0.03417486198425402 0.2382070722248819 chr5 180915260 6065315 0.03352572359014933 0.20021323508524533 chr6 171115067 5581847 0.03262042962002873 0.23978952053425592 chr7 159138663 5944063 0.037351470019576574 0.4063152043841172 chr8 146364022 5620929 0.038403761547356224 0.394074486777433 chr9 141213431 3449223 0.02442560155627123 0.21716494507258116 chr10 135534747 4239175 0.031277403719947916 0.3190060743067248 chr11 135006516 3640002 0.026961676427528877 0.2375927555459465 chr12 133851895 4997419 0.03733543705152624 0.21407800804777505 chr13 115169878 3218814 0.027948401577711144 0.18266660038115803 chr14 107349540 3548732 0.03305772898514516 0.20261545049770527 chr15 102531392 3860453 0.03765142484362253 0.2134249353663241 chr16 90354753 3611906 0.0399747205329641 0.23358036625200196 chr17 81195210 4393841 0.054114534588924644 0.26988714956069354 chr18 78077248 1957930 0.02507683160144169 0.3794691229485646 chr19 59128983 2655112 0.044903731897435135 0.3854167309884556 chr20 63025520 3362592 0.053352864046183196 0.265212289778605 chr21 48129895 1341200 0.027866256512714186 0.21972226686176774 chr22 51304566 958711 0.018686660364693467 0.1493548610650414 chrMT 16571 116427 7.025948946955524 4.7257175704500956 chrX 155270560 5442841 0.0350539149211544 0.2229292814934604 chrY 59373566 350264 0.005899325635923569 0.2256915142530393