BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080967.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 5,871,390 number of mapped reads = 5,066,629 (86.29%) number of supplementary alignments = 61,632 (1.05%) number of secondary alignments = 0 number of mapped bases = 342,673,512 bp number of sequenced bases = 342,548,042 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 429,384 duplication rate = 6.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1458 >>>>>>> ACTG content number of A's = 97,182,175 bp (28.37%) number of C's = 60,549,273 bp (17.68%) number of T's = 111,394,164 bp (32.52%) number of G's = 72,744,886 bp (21.24%) number of N's = 677,544 bp (0.2%) GC percentage = 38.91% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 3,428,350 number of insertions = 27,091 mapped reads with insertion percentage = 0.53% number of deletions = 76,675 mapped reads with deletion percentage = 1.5% homopolymer indels = 49.51% >>>>>>> Coverage mean coverageData = 0.1107X std coverageData = 0.7157X There is a 7.11% of reference with a coverageData >= 1X There is a 2.41% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 27563029 0.11058359208661711 1.0102648182377938 chr2 243199373 23191813 0.09536131904419014 0.6359541177890377 chr3 198022430 30628258 0.154670650188466 0.5642128583899256 chr4 191154276 21492748 0.11243665823096732 0.4971549300669813 chr5 180915260 19673514 0.10874435909939272 0.4690334667759069 chr6 171115067 28888881 0.16882721963928518 0.8240390988023375 chr7 159138663 16355252 0.10277359185806406 0.6258774748153247 chr8 146364022 26408900 0.1804330028591316 1.4540723811867946 chr9 141213431 17130841 0.1213116973271473 0.8299155162320956 chr10 135534747 15162743 0.11187347403983423 0.6054845019443773 chr11 135006516 15278544 0.1131689377126064 0.62990421852043 chr12 133851895 16749896 0.12513753354033574 0.5230290751564921 chr13 115169878 9223734 0.08008807650208677 0.40054314109556466 chr14 107349540 10067713 0.09378440745996676 0.5228510658209805 chr15 102531392 8805329 0.08587934707840503 0.4138064025848659 chr16 90354753 7501013 0.08301735936348584 0.4952319528354387 chr17 81195210 7056009 0.08690178891094684 0.4541554397305295 chr18 78077248 8327281 0.10665438669149814 1.3586418267310425 chr19 59128983 5951246 0.100648543202578 0.8034785384765624 chr20 63025520 5465875 0.08672479021196493 0.44536800228004236 chr21 48129895 7906724 0.16427885413005783 0.6624164958190255 chr22 51304566 2894948 0.05642671258538665 0.33074977535226996 chrMT 16571 85314 5.14839176875264 4.124937204313343 chrX 155270560 10136634 0.06528368288231845 0.40257741297237526 chrY 59373566 727273 0.012249104256261112 0.21433129622237332