BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525204.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 = 965,547 number of mapped reads = 874,881 (90.61%) number of supplementary alignments = 3,277 (0.34%) number of secondary alignments = 0 number of mapped bases = 50,200,401 bp number of sequenced bases = 50,187,238 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,529 duplication rate = 1.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8384 >>>>>>> ACTG content number of A's = 13,208,063 bp (26.32%) number of C's = 9,501,697 bp (18.93%) number of T's = 15,164,694 bp (30.22%) number of G's = 12,311,304 bp (24.53%) number of N's = 1,480 bp (0%) GC percentage = 43.46% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 244,194 number of insertions = 3,581 mapped reads with insertion percentage = 0.41% number of deletions = 7,952 mapped reads with deletion percentage = 0.9% homopolymer indels = 40.88% >>>>>>> Coverage mean coverageData = 0.0162X std coverageData = 0.171X There is a 1.52% of reference with a coverageData >= 1X There is a 0.07% 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 3588755 0.014398178771237646 0.25959622150076284 chr2 243199373 3914617 0.016096328504925875 0.18387028025789517 chr3 198022430 3036072 0.015331960121891242 0.12869882705790714 chr4 191154276 3169628 0.016581517642848858 0.14247935592636082 chr5 180915260 2795206 0.01545036057212642 0.1301053753803552 chr6 171115067 2646077 0.015463728860299602 0.1364092345238756 chr7 159138663 3275463 0.02058244639142155 0.21502094129387578 chr8 146364022 2180917 0.014900635895343187 0.16915469246745207 chr9 141213431 2311413 0.016368223501346695 0.17477356357711954 chr10 135534747 1952898 0.014408836429229473 0.17266951345321851 chr11 135006516 1923266 0.014245727221047612 0.1489254613061007 chr12 133851895 3774609 0.02819989212704086 0.1881358221705061 chr13 115169878 1892202 0.016429660540232576 0.13323415249018886 chr14 107349540 1782224 0.016602064619932234 0.1436619734195178 chr15 102531392 1262656 0.012314823542042616 0.11616035145392563 chr16 90354753 1419845 0.01571411522756307 0.1396896763949904 chr17 81195210 1478853 0.018213549789451864 0.1438500915081548 chr18 78077248 1588641 0.02034704143260787 0.2841857059488712 chr19 59128983 821677 0.013896349274263689 0.1970997710343909 chr20 63025520 1545131 0.024515957980195957 0.16623807256370163 chr21 48129895 605851 0.012587831326039668 0.12558083078892276 chr22 51304566 473607 0.00923128362493116 0.09958811512264683 chrMT 16571 1226 0.07398467201737977 0.27303036305643136 chrX 155270560 2619538 0.01687079636989781 0.14935970585181893 chrY 59373566 140029 0.002358440117947438 0.07025538971103604