BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514768.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 11,751,133 number of mapped reads = 3,404,954 (28.98%) number of supplementary alignments = 565,883 (4.82%) number of secondary alignments = 0 number of mapped bases = 310,206,408 bp number of sequenced bases = 309,938,084 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,590,644 duplication rate = 23.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2308 >>>>>>> ACTG content number of A's = 95,940,346 bp (30.95%) number of C's = 57,957,158 bp (18.7%) number of T's = 94,721,609 bp (30.56%) number of G's = 61,298,211 bp (19.78%) number of N's = 20,760 bp (0.01%) GC percentage = 38.48% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 1,850,937 number of insertions = 174,865 mapped reads with insertion percentage = 4.89% number of deletions = 87,098 mapped reads with deletion percentage = 2.37% homopolymer indels = 44.17% >>>>>>> Coverage mean coverageData = 0.1002X std coverageData = 10.1662X There is a 1.45% of reference with a coverageData >= 1X There is a 0.78% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.45% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.25% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.19% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 27696905 0.1111207060944494 3.4525521364444094 chr2 243199373 25725356 0.10577887468484551 4.116194982661566 chr3 198022430 24965082 0.1260719909355723 2.6969200855106226 chr4 191154276 23125323 0.1209772728285712 2.6848831636671457 chr5 180915260 18912924 0.10454023613044029 2.4774142514068025 chr6 171115067 15995867 0.09348017845792621 3.2673203632783867 chr7 159138663 10543742 0.06625506210266452 1.5679523847746395 chr8 146364022 10787640 0.07370417847631981 1.8643231568571847 chr9 141213431 25008163 0.17709479065061454 38.013863373724874 chr10 135534747 11618209 0.08572125788525654 3.8556692256974334 chr11 135006516 10660521 0.07896301094089414 1.8182327649563117 chr12 133851895 12430003 0.09286385523342797 3.0195645792363472 chr13 115169878 9866630 0.08567023054413586 1.9000851043238254 chr14 107349540 9656907 0.08995760019092769 2.1283699148732023 chr15 102531392 6993527 0.06820864189574252 1.8678731626409544 chr16 90354753 10213724 0.1130402514630304 2.8017358514015687 chr17 81195210 3348666 0.04124216194526746 1.314288653814797 chr18 78077248 7589413 0.09720389991204607 2.0256989534539342 chr19 59128983 9602383 0.16239722912196883 36.996078270338366 chr20 63025520 5719034 0.09074155992683598 2.831252036673332 chr21 48129895 1950793 0.040531835774833914 3.043065940748253 chr22 51304566 1549810 0.030208032556010705 3.1537876556342668 chrMT 16571 8554557 516.2366181884014 709.414104097859 chrX 155270560 14733265 0.09488769152375054 2.037917550019245 chrY 59373566 2957964 0.04981954427328822 1.9789275362360386