BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716448.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 = 1,077,139 number of mapped reads = 978,585 (90.85%) number of supplementary alignments = 19,969 (1.85%) number of secondary alignments = 0 number of mapped bases = 76,715,583 bp number of sequenced bases = 76,682,877 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,827 duplication rate = 2.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2307 >>>>>>> ACTG content number of A's = 19,338,155 bp (25.22%) number of C's = 14,765,510 bp (19.26%) number of T's = 23,908,246 bp (31.18%) number of G's = 18,666,417 bp (24.34%) number of N's = 4,549 bp (0.01%) GC percentage = 43.6% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 615,789 number of insertions = 7,203 mapped reads with insertion percentage = 0.73% number of deletions = 18,916 mapped reads with deletion percentage = 1.9% homopolymer indels = 43.05% >>>>>>> Coverage mean coverageData = 0.0248X std coverageData = 0.316X There is a 2.23% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6130984 0.024597667903102235 0.5417616894678832 chr2 243199373 6589600 0.027095464592336756 0.43743517515139635 chr3 198022430 5062482 0.025565194811517058 0.17513354244542675 chr4 191154276 4938121 0.025833170480580828 0.18602241291975505 chr5 180915260 4566394 0.025240513155164467 0.1748314212799594 chr6 171115067 4413406 0.025792036185802388 0.2084493984869041 chr7 159138663 4287391 0.02694122797801814 0.409082550374316 chr8 146364022 3913802 0.02674019165720931 0.3833925079080653 chr9 141213431 3252139 0.02302995527387193 0.3304168832018505 chr10 135534747 3654730 0.02696526227329734 0.3126978700082555 chr11 135006516 3449576 0.02555118154445227 0.30768663852892764 chr12 133851895 3476511 0.025972818688894915 0.17661789586341103 chr13 115169878 2351005 0.02041336711323077 0.1520228873351366 chr14 107349540 2311297 0.021530571998724914 0.19546924100346375 chr15 102531392 2148418 0.020953758240208033 0.1584412417710435 chr16 90354753 2252182 0.024925993655253532 0.20065573228086458 chr17 81195210 2036720 0.025084238343616574 0.19059384875298735 chr18 78077248 2128316 0.027259106263581422 0.6218768642504996 chr19 59128983 1641101 0.02775459540712885 0.3959874662037089 chr20 63025520 1530201 0.024279069811720712 0.17724379673467497 chr21 48129895 981808 0.020399130311836332 0.16465556020713745 chr22 51304566 858950 0.01674217456590511 0.13911786462267356 chrMT 16571 2787 0.16818538410476133 0.5252807057525144 chrX 155270560 4524455 0.029139168429610868 0.24947739646353406 chrY 59373566 213207 0.0035909414637483625 0.10619141015051865