BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525168.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 = 628,623 number of mapped reads = 590,302 (93.9%) number of supplementary alignments = 2,007 (0.32%) number of secondary alignments = 0 number of mapped bases = 36,760,829 bp number of sequenced bases = 36,748,261 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,769 duplication rate = 1.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7048 >>>>>>> ACTG content number of A's = 9,471,713 bp (25.77%) number of C's = 7,324,292 bp (19.93%) number of T's = 11,130,821 bp (30.29%) number of G's = 8,820,453 bp (24%) number of N's = 982 bp (0%) GC percentage = 43.93% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 177,962 number of insertions = 2,623 mapped reads with insertion percentage = 0.44% number of deletions = 7,809 mapped reads with deletion percentage = 1.31% homopolymer indels = 43.34% >>>>>>> Coverage mean coverageData = 0.0119X std coverageData = 0.1421X There is a 1.13% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 3782879 0.01517700932829371 0.22436289399032477 chr2 243199373 2954017 0.012146482795414115 0.14177841726911952 chr3 198022430 3372100 0.017028879001232334 0.13633837907071192 chr4 191154276 1805540 0.009445459645380886 0.10211601182636525 chr5 180915260 1597879 0.008832195802609464 0.09686030163825243 chr6 171115067 2263927 0.013230436335568276 0.12507011566733892 chr7 159138663 2693261 0.016923989112564052 0.24097665346447766 chr8 146364022 2050136 0.014007103466998195 0.1366181645613642 chr9 141213431 1201888 0.008511145090724408 0.11178756906697644 chr10 135534747 1958918 0.014453253083506328 0.16413148510768857 chr11 135006516 1637490 0.012128970130597253 0.12473701805684696 chr12 133851895 1522139 0.011371815094586445 0.11048543951437505 chr13 115169878 1097885 0.009532744317051374 0.10027657768091962 chr14 107349540 1304564 0.012152488031155047 0.11676342495320352 chr15 102531392 976340 0.009522351944661007 0.1013053986157384 chr16 90354753 960975 0.010635577743209591 0.11333939794334533 chr17 81195210 705933 0.008694269033850642 0.09890053666894738 chr18 78077248 810044 0.010374904607293536 0.18003672144027866 chr19 59128983 537294 0.009086812807181209 0.1643287829493558 chr20 63025520 661282 0.0104922894725819 0.1067028923136825 chr21 48129895 461782 0.009594494232742456 0.10468663234347192 chr22 51304566 288639 0.005625990482016747 0.07702119378874378 chrMT 16571 21428 1.293102407820892 1.3668883610468556 chrX 155270560 1991617 0.012826752218836592 0.12056716256172453 chrY 59373566 102872 0.0017326228982102912 0.0615040218464868