BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524800.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 = 1,580,332 number of mapped reads = 1,437,059 (90.93%) number of supplementary alignments = 4,534 (0.29%) number of secondary alignments = 0 number of mapped bases = 82,028,093 bp number of sequenced bases = 82,001,792 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,138 duplication rate = 2.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5406 >>>>>>> ACTG content number of A's = 19,606,535 bp (23.91%) number of C's = 15,173,185 bp (18.5%) number of T's = 27,921,885 bp (34.05%) number of G's = 19,298,424 bp (23.53%) number of N's = 1,763 bp (0%) GC percentage = 42.04% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 420,106 number of insertions = 6,006 mapped reads with insertion percentage = 0.42% number of deletions = 16,854 mapped reads with deletion percentage = 1.17% homopolymer indels = 43.67% >>>>>>> Coverage mean coverageData = 0.0265X std coverageData = 0.271X There is a 2.41% of reference with a coverageData >= 1X There is a 0.16% 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 9408024 0.037745237954693 0.49992409686136763 chr2 243199373 6769655 0.02783582423133961 0.3365225011755143 chr3 198022430 6207314 0.031346519684664 0.19300155089609644 chr4 191154276 4781414 0.02501337715301749 0.17610947451306538 chr5 180915260 3784252 0.02091726259023147 0.1561770543175263 chr6 171115067 5185408 0.030303631882983163 0.21274997853845995 chr7 159138663 4896707 0.030770064971577648 0.42645538964688157 chr8 146364022 4733824 0.03234281167813221 0.2766016445466926 chr9 141213431 2712234 0.019206629148469597 0.20232818380053696 chr10 135534747 4356704 0.032144554045613116 0.3106131429812205 chr11 135006516 3754600 0.027810509531258475 0.21900720593892767 chr12 133851895 3650372 0.027271724468301325 0.18121018594780755 chr13 115169878 2639826 0.022921149573502195 0.16570469447060887 chr14 107349540 3053816 0.02844740648166727 0.18536011263340174 chr15 102531392 2201484 0.021471316804125708 0.16232048004026503 chr16 90354753 2133268 0.023609914577487696 0.18581169003380296 chr17 81195210 1796299 0.022123213918653576 0.16428624195779226 chr18 78077248 1771738 0.022692116402463366 0.3604978075646071 chr19 59128983 1350073 0.022832677504363637 0.35011323634292857 chr20 63025520 1431582 0.022714322706103813 0.1645164255189647 chr21 48129895 1047331 0.021760508723320506 0.16446117614606984 chr22 51304566 644884 0.01256971942809145 0.11999945564022314 chrMT 16571 78961 4.765011164081829 3.2688157208872375 chrX 155270560 3423917 0.022051295493492135 0.1798943804752674 chrY 59373566 214406 0.0036111356356800265 0.09723832178605939