BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013305.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 = 1,938,054 number of mapped reads = 1,703,406 (87.89%) number of supplementary alignments = 13,717 (0.71%) number of secondary alignments = 0 number of mapped bases = 112,272,085 bp number of sequenced bases = 112,220,991 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,577 duplication rate = 3.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7038 >>>>>>> ACTG content number of A's = 30,760,479 bp (27.41%) number of C's = 20,673,068 bp (18.42%) number of T's = 35,669,314 bp (31.78%) number of G's = 25,116,532 bp (22.38%) number of N's = 1,598 bp (0%) GC percentage = 40.8% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 802,926 number of insertions = 7,481 mapped reads with insertion percentage = 0.44% number of deletions = 29,502 mapped reads with deletion percentage = 1.71% homopolymer indels = 46.21% >>>>>>> Coverage mean coverageData = 0.0363X std coverageData = 0.3629X There is a 2.95% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 11552458 0.046348763159149764 0.828579973115246 chr2 243199373 11556466 0.047518485995438814 0.4224654084819439 chr3 198022430 9831971 0.04965079460947934 0.2660512308359599 chr4 191154276 3667480 0.019185968929096832 0.1680768335474732 chr5 180915260 5245543 0.028994475092924722 0.20220251478003068 chr6 171115067 4204798 0.024572926707850922 0.20123790347994938 chr7 159138663 9367836 0.058865870954313594 0.43941744970657487 chr8 146364022 7166769 0.0489653734713576 0.402999061501346 chr9 141213431 3331358 0.023590942988985234 0.2550798608265004 chr10 135534747 4948507 0.036510984153753576 0.33554555545786535 chr11 135006516 5367760 0.03975926613793959 0.277092537876721 chr12 133851895 4789874 0.0357848799974031 0.22586460321377633 chr13 115169878 3815450 0.033128888093464856 0.2150544471580227 chr14 107349540 4991940 0.04650173629062593 0.26093059691322545 chr15 102531392 1178223 0.011491339159815562 0.128918200008331 chr16 90354753 1966166 0.021760515465080184 0.17729547023145478 chr17 81195210 2432629 0.029960252581402277 0.21373370784329754 chr18 78077248 3113933 0.03988271973930229 0.3315775217524625 chr19 59128983 1386078 0.023441600543002743 0.49899740997565184 chr20 63025520 4197818 0.06660505141409384 0.31240507968781134 chr21 48129895 1521427 0.031610852257209374 0.2135469561617171 chr22 51304566 1079671 0.021044345253792812 0.1695843749600859 chrMT 16571 12727 0.7680284834952628 1.1588160894858717 chrX 155270560 5358969 0.03451374813100436 0.2325678191738919 chrY 59373566 186234 0.003136648386590086 0.06879699990444586