BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524326.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 = 3,949,006 number of mapped reads = 3,632,076 (91.97%) number of supplementary alignments = 16,723 (0.42%) number of secondary alignments = 0 number of mapped bases = 211,417,111 bp number of sequenced bases = 211,362,793 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 187,327 duplication rate = 3.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7299 >>>>>>> ACTG content number of A's = 49,396,991 bp (23.37%) number of C's = 40,465,605 bp (19.15%) number of T's = 67,071,457 bp (31.73%) number of G's = 54,399,507 bp (25.74%) number of N's = 29,233 bp (0.01%) GC percentage = 44.88% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,048,487 number of insertions = 12,927 mapped reads with insertion percentage = 0.35% number of deletions = 34,013 mapped reads with deletion percentage = 0.93% homopolymer indels = 42.88% >>>>>>> Coverage mean coverageData = 0.0683X std coverageData = 0.5531X There is a 5.69% of reference with a coverageData >= 1X There is a 0.78% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 18288537 0.07337408800277372 1.0985016677499106 chr2 243199373 13714608 0.05639244801835899 0.7693391400917695 chr3 198022430 14534242 0.07339694801240446 0.32092872065019684 chr4 191154276 11028897 0.05769631331710309 0.33205744614119953 chr5 180915260 12413382 0.0686143446384788 0.3078335906625024 chr6 171115067 13379930 0.07819258838264663 0.37602120236133757 chr7 159138663 9762549 0.06134617958930571 0.7224783779782826 chr8 146364022 20434283 0.13961274581536165 0.6429997001822311 chr9 141213431 8896221 0.06299840558367284 0.41583461913357717 chr10 135534747 10883151 0.08029786634714417 0.5335560099299781 chr11 135006516 10365042 0.07677438324532425 0.4579863166999287 chr12 133851895 8581407 0.06411121037920307 0.30681129597602325 chr13 115169878 5369001 0.04661810095865518 0.25365188042281944 chr14 107349540 4501211 0.04193041721464293 0.2741153825397133 chr15 102531392 6489585 0.06329363986397454 0.30473122620214416 chr16 90354753 6753057 0.0747393665057111 0.35398470569834706 chr17 81195210 6531316 0.08043967125646943 0.3932371704897257 chr18 78077248 4986457 0.06386568594220944 0.8005203120110549 chr19 59128983 3967642 0.06710147543041625 0.7462337956643255 chr20 63025520 4975703 0.07894743272249083 0.3388647443188991 chr21 48129895 3088048 0.06416070510854013 0.3372669759414617 chr22 51304566 1630946 0.03178949023757457 0.20857462201158916 chrMT 16571 18355 1.1076579566712932 1.2566385952720438 chrX 155270560 10238293 0.0659384045500963 0.35762429212766805 chrY 59373566 585248 0.009857046484288985 0.25526420394274346