BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234112.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 = 681,901 number of mapped reads = 460,674 (67.56%) number of supplementary alignments = 1,834 (0.27%) number of secondary alignments = 0 number of mapped bases = 29,860,937 bp number of sequenced bases = 29,848,288 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,925 duplication rate = 1.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1818 >>>>>>> ACTG content number of A's = 8,431,053 bp (28.25%) number of C's = 5,077,990 bp (17.01%) number of T's = 9,622,428 bp (32.24%) number of G's = 6,710,921 bp (22.48%) number of N's = 5,896 bp (0.02%) GC percentage = 39.5% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 269,798 number of insertions = 2,367 mapped reads with insertion percentage = 0.51% number of deletions = 7,276 mapped reads with deletion percentage = 1.57% homopolymer indels = 46.86% >>>>>>> Coverage mean coverageData = 0.0096X std coverageData = 0.1196X There is a 0.91% 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 3181847 0.012765653249866928 0.16889574934210702 chr2 243199373 1644347 0.006761312661772364 0.10792933081213679 chr3 198022430 3062626 0.015466056042237235 0.1289782584312577 chr4 191154276 1480383 0.007744440935237044 0.09201638431949798 chr5 180915260 1673233 0.009248711247464698 0.09959611376592326 chr6 171115067 1861666 0.010879614709790576 0.11491306525864188 chr7 159138663 2087899 0.01311999837525341 0.15273951018722415 chr8 146364022 1479304 0.010107019332934154 0.18836441124511136 chr9 141213431 1116514 0.00790657087001873 0.10060410560440818 chr10 135534747 1124813 0.008299074775267777 0.10831279063417922 chr11 135006516 1237182 0.009163868801710282 0.10530426161969941 chr12 133851895 981612 0.0073335681949067665 0.08887140535104343 chr13 115169878 907012 0.00787542728837483 0.09203994389681931 chr14 107349540 1605169 0.014952732913434002 0.12787530245639206 chr15 102531392 590920 0.00576330808031944 0.07874866334785861 chr16 90354753 523593 0.005794858406618631 0.08224299785610932 chr17 81195210 638303 0.007861338125734264 0.09286310661342943 chr18 78077248 704453 0.0090225131910387 0.13980651353886583 chr19 59128983 759814 0.012850111086808308 0.13588546873316804 chr20 63025520 685945 0.01088360714834245 0.10842823747914228 chr21 48129895 534394 0.01110316155894377 0.11072886423904403 chr22 51304566 269072 0.0052446014259237665 0.07507728635361405 chrMT 16571 24483 1.4774606239816548 1.5643048710788652 chrX 155270560 1613663 0.010392588266571589 0.10740500902300373 chrY 59373566 72690 0.0012242821999271527 0.038882355591569565