BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716229.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 = 1,105,361 number of mapped reads = 991,766 (89.72%) number of supplementary alignments = 4,229 (0.38%) number of secondary alignments = 0 number of mapped bases = 56,810,919 bp number of sequenced bases = 56,794,673 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,983 duplication rate = 2.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5515 >>>>>>> ACTG content number of A's = 13,880,350 bp (24.44%) number of C's = 10,082,626 bp (17.75%) number of T's = 18,600,421 bp (32.75%) number of G's = 14,230,323 bp (25.06%) number of N's = 953 bp (0%) GC percentage = 42.81% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 308,968 number of insertions = 3,889 mapped reads with insertion percentage = 0.39% number of deletions = 9,659 mapped reads with deletion percentage = 0.97% homopolymer indels = 43.16% >>>>>>> Coverage mean coverageData = 0.0184X std coverageData = 0.1924X There is a 1.7% of reference with a coverageData >= 1X There is a 0.1% 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 4533050 0.01818671496910734 0.3223540829145438 chr2 243199373 4817136 0.019807353697412697 0.20650670489451117 chr3 198022430 3789072 0.01913455965569153 0.1460462178251804 chr4 191154276 3761831 0.019679554539496675 0.15992728229236566 chr5 180915260 3472696 0.01919515247083082 0.14682337775373966 chr6 171115067 3316784 0.01938335447690296 0.15727933467731595 chr7 159138663 3128691 0.019660156375701107 0.21429278936898966 chr8 146364022 2901299 0.019822487523607407 0.2116635995549854 chr9 141213431 2383302 0.016877303972594505 0.19163296591271806 chr10 135534747 2686107 0.019818585709242515 0.1951538665664918 chr11 135006516 2598308 0.01924579699545761 0.184358649737777 chr12 133851895 2573728 0.019228177531591912 0.1493982168432483 chr13 115169878 1817464 0.01578072349785766 0.13245539393000744 chr14 107349540 1725497 0.016073631987617274 0.14535884089071843 chr15 102531392 1589716 0.015504675875267547 0.1322964923425429 chr16 90354753 1609117 0.01780888051345788 0.150595746159859 chr17 81195210 1454163 0.017909467812202224 0.14774635918994197 chr18 78077248 1561569 0.020000307900196482 0.3149136635392163 chr19 59128983 1112778 0.01881950176616432 0.24898740224954496 chr20 63025520 1161773 0.01843337429028749 0.14780426781616882 chr21 48129895 748301 0.015547530282374395 0.14087285558143398 chr22 51304566 627679 0.012234369159267422 0.11622807129818123 chrMT 16571 2712 0.16365940498461168 0.43364587095523 chrX 155270560 3252739 0.020948845679438523 0.17148285400634167 chrY 59373566 185407 0.0031227196291359694 0.08320057269895743