BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238036.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,468,827 number of mapped reads = 1,289,396 (87.78%) number of supplementary alignments = 10,758 (0.73%) number of secondary alignments = 0 number of mapped bases = 84,386,428 bp number of sequenced bases = 84,344,666 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 135,820 duplication rate = 8.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2158 >>>>>>> ACTG content number of A's = 22,952,806 bp (27.21%) number of C's = 15,301,435 bp (18.14%) number of T's = 26,931,193 bp (31.93%) number of G's = 19,007,515 bp (22.54%) number of N's = 151,717 bp (0.18%) GC percentage = 40.68% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 714,170 number of insertions = 7,216 mapped reads with insertion percentage = 0.55% number of deletions = 25,320 mapped reads with deletion percentage = 1.94% homopolymer indels = 48.2% >>>>>>> Coverage mean coverageData = 0.0273X std coverageData = 0.2731X There is a 1.83% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.07% 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% 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 2206655 0.008853157481200418 0.21459291623058183 chr2 243199373 8861162 0.03643579294918659 0.42387618066278354 chr3 198022430 4521990 0.022835746435391182 0.21160506092218662 chr4 191154276 6334101 0.033136067539498826 0.25922881014472526 chr5 180915260 1684891 0.009313150256092272 0.1325495203583585 chr6 171115067 7067835 0.04130457430729931 0.3374741371403116 chr7 159138663 6094950 0.0382996179878676 0.3723968460048393 chr8 146364022 3835479 0.02620506698018998 0.34249755032334683 chr9 141213431 1187993 0.008412747934720176 0.16561291479762902 chr10 135534747 7608441 0.0561364607114366 0.3461894014478413 chr11 135006516 3628690 0.02687788787913022 0.2329469307465877 chr12 133851895 4286058 0.03202089891966042 0.252195874079628 chr13 115169878 1468597 0.01275157207338537 0.15996385692897994 chr14 107349540 2987587 0.02783045926419433 0.237791925568833 chr15 102531392 4503249 0.04392068528631699 0.29407441188267375 chr16 90354753 1152019 0.012749954615005145 0.15628236038953802 chr17 81195210 4490909 0.05531002383022348 0.32759964078543297 chr18 78077248 3029999 0.03880770746427948 0.30887209718718706 chr19 59128983 2506044 0.0423826670585557 0.3016346488535751 chr20 63025520 2100563 0.03332876904466635 0.25866663524927774 chr21 48129895 1583310 0.032896601997573445 0.25899741700582213 chr22 51304566 996582 0.019424820784957036 0.18932115588814327 chrMT 16571 8537 0.5151771166495686 0.8230368507588163 chrX 155270560 2062524 0.013283419599955071 0.16272547394570389 chrY 59373566 178263 0.003002396723147806 0.09116296221905552