BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231812.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 = 5,196,734 number of mapped reads = 4,886,656 (94.03%) number of supplementary alignments = 31,591 (0.61%) number of secondary alignments = 0 number of mapped bases = 317,253,532 bp number of sequenced bases = 317,133,497 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 547,355 duplication rate = 9.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7153 >>>>>>> ACTG content number of A's = 83,934,182 bp (26.47%) number of C's = 57,822,668 bp (18.23%) number of T's = 102,247,916 bp (32.24%) number of G's = 73,003,991 bp (23.02%) number of N's = 124,740 bp (0.04%) GC percentage = 41.25% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,939,407 number of insertions = 22,286 mapped reads with insertion percentage = 0.45% number of deletions = 68,590 mapped reads with deletion percentage = 1.39% homopolymer indels = 44.89% >>>>>>> Coverage mean coverageData = 0.1025X std coverageData = 0.9161X There is a 7.45% of reference with a coverageData >= 1X There is a 1.83% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% 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 27095331 0.10870717549786968 1.4167880906766188 chr2 243199373 17582995 0.07229868557268032 1.4024839229315162 chr3 198022430 42691717 0.21559030964320558 0.6236244336557732 chr4 191154276 10040462 0.05252543762086703 0.39281920372031254 chr5 180915260 14781473 0.08170384853107471 0.3799236072001449 chr6 171115067 21219559 0.12400754283081337 0.7115466073741574 chr7 159138663 19677581 0.12365053613652642 1.6296369255254592 chr8 146364022 18111661 0.12374394166347792 1.4613845657542797 chr9 141213431 13045339 0.0923802991515729 0.6230475696575044 chr10 135534747 18490747 0.1364280924949821 0.81802001388182 chr11 135006516 9892113 0.07327137454609968 0.65010721639586 chr12 133851895 12365880 0.09238479589698749 0.4114867175929677 chr13 115169878 13490830 0.11713852818355855 0.49084381307276737 chr14 107349540 16890575 0.15734184794830047 0.5699427866697753 chr15 102531392 6010955 0.058625508566196 0.39842918353260076 chr16 90354753 11174428 0.12367282991742559 0.5251036297510888 chr17 81195210 6677918 0.08224522111587618 0.43395231786700306 chr18 78077248 5662145 0.07251978194723256 1.58309034916119 chr19 59128983 7765600 0.1313332245203676 0.9272035366286943 chr20 63025520 6871540 0.10902789854014691 0.4938014077770072 chr21 48129895 4827962 0.10031108524130376 0.4383797893796565 chr22 51304566 2963612 0.05776507299564721 0.30295062942720213 chrMT 16571 378041 22.813408967473297 13.922369447766869 chrX 155270560 8939031 0.057570675342447405 0.39759839890910836 chrY 59373566 606037 0.010207185467014058 0.2133825400297223