BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524441.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 = 2,741,736 number of mapped reads = 2,533,595 (92.41%) number of supplementary alignments = 5,659 (0.21%) number of secondary alignments = 0 number of mapped bases = 147,814,322 bp number of sequenced bases = 147,767,957 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 154,577 duplication rate = 4.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0188 >>>>>>> ACTG content number of A's = 36,827,563 bp (24.92%) number of C's = 27,291,766 bp (18.47%) number of T's = 47,569,683 bp (32.19%) number of G's = 36,076,079 bp (24.41%) number of N's = 2,866 bp (0%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 680,448 number of insertions = 11,076 mapped reads with insertion percentage = 0.43% number of deletions = 27,264 mapped reads with deletion percentage = 1.07% homopolymer indels = 41.46% >>>>>>> Coverage mean coverageData = 0.0477X std coverageData = 0.4038X There is a 4.01% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 11858251 0.047575612660158625 0.7511496354152085 chr2 243199373 12706819 0.052248568091497506 0.46824848842928013 chr3 198022430 9842255 0.049702728120243754 0.259328712580172 chr4 191154276 9595156 0.05019587424766789 0.31010163371537447 chr5 180915260 8847909 0.048906371966632334 0.25945826236179487 chr6 171115067 8422327 0.04922025364370748 0.32992875940409716 chr7 159138663 8268692 0.05195903901743852 0.5732569371487393 chr8 146364022 7692766 0.05255913232556564 0.38827234651009884 chr9 141213431 6190196 0.04383574534068222 0.34618941732438546 chr10 135534747 7076860 0.05221435946606371 0.39163316970989204 chr11 135006516 6627013 0.04908661593785592 0.3900992955736965 chr12 133851895 6616891 0.04943442152985582 0.2634364858803838 chr13 115169878 4611282 0.040038958797889844 0.23781779605950262 chr14 107349540 4472389 0.04166192980426372 0.24258434368893586 chr15 102531392 4235332 0.04130766116976155 0.2534213736651553 chr16 90354753 4277540 0.04734161577532064 0.277936666169384 chr17 81195210 3939760 0.04852207414698478 0.27825628890396614 chr18 78077248 3972127 0.05087432128755358 0.619321301248067 chr19 59128983 2883617 0.048768249573986414 0.5232300958131236 chr20 63025520 3150084 0.049981087026334726 0.2673362207311121 chr21 48129895 1963155 0.04078868237713795 0.2597453074855121 chr22 51304566 1720201 0.033529198941084505 0.21319933265376761 chrMT 16571 15318 0.9243859754993664 1.2077200133465968 chrX 155270560 8378250 0.05395903769523341 0.31228484636618514 chrY 59373566 450132 0.007581353627976463 0.19008865003303813