BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716783.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 = 1,248,161 number of mapped reads = 892,234 (71.48%) number of supplementary alignments = 19,546 (1.57%) number of secondary alignments = 0 number of mapped bases = 67,431,932 bp number of sequenced bases = 67,407,898 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,736 duplication rate = 1.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5652 >>>>>>> ACTG content number of A's = 17,854,826 bp (26.49%) number of C's = 13,694,158 bp (20.32%) number of T's = 20,359,226 bp (30.2%) number of G's = 15,491,105 bp (22.98%) number of N's = 8,583 bp (0.01%) GC percentage = 43.3% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 495,326 number of insertions = 5,929 mapped reads with insertion percentage = 0.65% number of deletions = 14,031 mapped reads with deletion percentage = 1.55% homopolymer indels = 39.46% >>>>>>> Coverage mean coverageData = 0.0218X std coverageData = 0.2025X There is a 1.99% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% 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 5376523 0.021570750670266134 0.22275399981439195 chr2 243199373 5815899 0.023914120041748626 0.28646395231862243 chr3 198022430 4561069 0.02303309276630935 0.16148943728276433 chr4 191154276 4390116 0.022966349965406998 0.1710193657820841 chr5 180915260 4125044 0.022800973229123955 0.16193161050107172 chr6 171115067 3849036 0.022493846202333544 0.17351790466868677 chr7 159138663 3640369 0.022875452962678216 0.2215540782463939 chr8 146364022 3420597 0.02337047693319059 0.2585798558131974 chr9 141213431 2892935 0.020486259554163798 0.21658855777179137 chr10 135534747 3150582 0.023245566688518626 0.19296801178372922 chr11 135006516 3056541 0.0226399516894429 0.2177002502471097 chr12 133851895 2971257 0.022198094393807426 0.16009987133819562 chr13 115169878 2168789 0.018831217308400726 0.14589729461907772 chr14 107349540 2052617 0.019120873736394213 0.16540125129732294 chr15 102531392 1959641 0.01911259529179122 0.14720111460230578 chr16 90354753 1988811 0.022011138694607465 0.1685834894406987 chr17 81195210 1835444 0.022605323639165415 0.17103361374773499 chr18 78077248 1858759 0.023806666443981224 0.3552462837517672 chr19 59128983 1310712 0.02216699718985527 0.21029853273322094 chr20 63025520 1440247 0.02285180669671587 0.16438833367106834 chr21 48129895 888389 0.01845815371091086 0.15248816050336342 chr22 51304566 752526 0.014667817285502425 0.1294323681146005 chrMT 16571 4184 0.2524892885160823 0.5552882037727915 chrX 155270560 3753011 0.02417078292240332 0.1892148157780392 chrY 59373566 168834 0.00284358867715643 0.09290148702341867