BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013232.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 = 1,018,210 number of mapped reads = 905,053 (88.89%) number of supplementary alignments = 5,537 (0.54%) number of secondary alignments = 0 number of mapped bases = 62,170,766 bp number of sequenced bases = 62,144,159 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,781 duplication rate = 2.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7749 >>>>>>> ACTG content number of A's = 18,037,675 bp (29.03%) number of C's = 11,237,892 bp (18.08%) number of T's = 19,976,515 bp (32.15%) number of G's = 12,877,981 bp (20.72%) number of N's = 14,096 bp (0.02%) GC percentage = 38.81% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 506,991 number of insertions = 4,924 mapped reads with insertion percentage = 0.54% number of deletions = 15,274 mapped reads with deletion percentage = 1.67% homopolymer indels = 47.64% >>>>>>> Coverage mean coverageData = 0.0201X std coverageData = 0.2473X There is a 1.83% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% 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 4355059 0.017472610429323663 0.39205503582149304 chr2 243199373 7743289 0.031839263829023114 0.27669462967496466 chr3 198022430 4899368 0.024741480043447603 0.1668923196604625 chr4 191154276 4920904 0.02574310187024014 0.17911310620442122 chr5 180915260 2807286 0.015517132164528298 0.13227875924864219 chr6 171115067 3884165 0.022699140806811593 0.19870048186661524 chr7 159138663 3825029 0.024035824656890577 0.4363914408445882 chr8 146364022 4039506 0.027599036599308537 0.39741055680691084 chr9 141213431 2431382 0.017217781501251108 0.21654606128214998 chr10 135534747 2356650 0.01738779207666946 0.254015757666393 chr11 135006516 2380804 0.01763473401535671 0.17131979292314917 chr12 133851895 3157589 0.023590170314734805 0.16675486264784573 chr13 115169878 1234791 0.010721475280194358 0.109963669434634 chr14 107349540 2177695 0.02028602078779285 0.15690985738325017 chr15 102531392 1151556 0.01123125296104436 0.11284308772071358 chr16 90354753 1281542 0.014183448655988246 0.1435243465164697 chr17 81195210 1705622 0.02100643621711182 0.16205712854581464 chr18 78077248 1610714 0.02062974863048452 0.41037092560825716 chr19 59128983 794262 0.013432701861285184 0.28069704332923023 chr20 63025520 991104 0.015725439472772298 0.13839318611714965 chr21 48129895 919637 0.019107396764526496 0.15577760136186972 chr22 51304566 573058 0.011169727076533499 0.11130215763414018 chrMT 16571 22559 1.3613541729527487 1.449958796616055 chrX 155270560 2794173 0.017995510546236194 0.1548103150972052 chrY 59373566 113022 0.0019035743953799238 0.06641097538297719