BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524912.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 = 1,594,033 number of mapped reads = 1,478,540 (92.75%) number of supplementary alignments = 6,290 (0.39%) number of secondary alignments = 0 number of mapped bases = 86,243,203 bp number of sequenced bases = 86,214,552 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,736 duplication rate = 4.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8914 >>>>>>> ACTG content number of A's = 21,177,953 bp (24.56%) number of C's = 16,162,641 bp (18.75%) number of T's = 27,769,468 bp (32.21%) number of G's = 21,103,860 bp (24.48%) number of N's = 630 bp (0%) GC percentage = 43.23% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 431,727 number of insertions = 5,198 mapped reads with insertion percentage = 0.35% number of deletions = 17,174 mapped reads with deletion percentage = 1.15% homopolymer indels = 42.92% >>>>>>> Coverage mean coverageData = 0.0279X std coverageData = 0.2655X There is a 2.43% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% 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 8456550 0.03392789942136192 0.4864945578363496 chr2 243199373 7563953 0.03110186061211597 0.31406451556564946 chr3 198022430 5383713 0.027187389832555836 0.18365324504615343 chr4 191154276 3899922 0.020401960560903175 0.20114234037144307 chr5 180915260 5257163 0.029058704058463614 0.19027643642992928 chr6 171115067 5508736 0.03219316741990932 0.21246871040322118 chr7 159138663 5174728 0.032517101139652026 0.3209909750325301 chr8 146364022 7455151 0.050935680081270245 0.35716363358576986 chr9 141213431 3140070 0.022236340961080396 0.21267307440411837 chr10 135534747 3714553 0.027406647241537258 0.2761853561002738 chr11 135006516 5415359 0.040111834305834544 0.2556979297509134 chr12 133851895 2868888 0.02143330133652572 0.1692767268267667 chr13 115169878 2082870 0.018085197589598905 0.14989652771093404 chr14 107349540 1592959 0.014838992323581452 0.14196102321743684 chr15 102531392 2187596 0.021335865604945655 0.16398496179065847 chr16 90354753 2539027 0.028100646791652455 0.1954267501907113 chr17 81195210 1932873 0.023805258955546763 0.17906855428259102 chr18 78077248 2247794 0.028789359993835847 0.34118704772664826 chr19 59128983 1760096 0.02976706025875669 0.3311212279243666 chr20 63025520 1605096 0.025467397968315056 0.18266116865633425 chr21 48129895 772384 0.016047905361106646 0.1729987724067778 chr22 51304566 1586249 0.030918281230563376 0.19854363944725448 chrMT 16571 8787 0.5302637137167341 0.862652612353207 chrX 155270560 3834575 0.024696085336460435 0.19010549091656204 chrY 59373566 254111 0.004279867576085964 0.15757045109323561