BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080794.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 = 1,789,002 number of mapped reads = 1,555,350 (86.94%) number of supplementary alignments = 19,267 (1.08%) number of secondary alignments = 0 number of mapped bases = 102,393,866 bp number of sequenced bases = 102,359,631 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,734 duplication rate = 1.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5655 >>>>>>> ACTG content number of A's = 29,842,956 bp (29.16%) number of C's = 19,885,837 bp (19.43%) number of T's = 29,946,579 bp (29.26%) number of G's = 22,682,327 bp (22.16%) number of N's = 1,932 bp (0%) GC percentage = 41.59% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 797,903 number of insertions = 8,761 mapped reads with insertion percentage = 0.56% number of deletions = 21,153 mapped reads with deletion percentage = 1.35% homopolymer indels = 43.36% >>>>>>> Coverage mean coverageData = 0.0331X std coverageData = 0.3707X There is a 3.03% of reference with a coverageData >= 1X There is a 0.18% 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 12799030 0.051350042574216895 0.8017987116470842 chr2 243199373 7618934 0.03132793438575189 0.3497116363438369 chr3 198022430 6037167 0.030487288737947513 0.1857588697838372 chr4 191154276 5898536 0.03085746300543128 0.19243694971555264 chr5 180915260 7816080 0.04320298906792053 0.22064935243359854 chr6 171115067 7078517 0.041367000136814366 0.31309466573800127 chr7 159138663 7153848 0.04495355097962586 0.6082057083441852 chr8 146364022 4551813 0.031099261538467423 0.33463537889818123 chr9 141213431 3571258 0.02528978989257757 0.28496084354511025 chr10 135534747 4227357 0.03119020836774794 0.3284137692146964 chr11 135006516 4121299 0.03052666732026475 0.26613741915178063 chr12 133851895 3914753 0.02924690009058146 0.18373745908569714 chr13 115169878 4147107 0.03600860808413811 0.20028750711745907 chr14 107349540 2711120 0.02525506862907843 0.1924804112087581 chr15 102531392 2556431 0.024933154130980687 0.17557911151075845 chr16 90354753 2407410 0.02664397743414782 0.20542128102925408 chr17 81195210 2568790 0.03163721111134511 0.20768417720319943 chr18 78077248 1474350 0.018883221908641043 0.5854966011852929 chr19 59128983 1768549 0.029910018915765894 0.5890006062373137 chr20 63025520 1750303 0.027771337705742055 0.18669565426269322 chr21 48129895 1607810 0.03340564113011259 0.20534361149423178 chr22 51304566 644484 0.012561922851077231 0.11594384780015926 chrMT 16571 32444 1.9578782209884737 1.7787726700517072 chrX 155270560 5689825 0.03664458349348389 0.23376225625562927 chrY 59373566 246651 0.004154222436294293 0.08748511508170032