BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714160.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 779,760 number of mapped reads = 695,442 (89.19%) number of supplementary alignments = 20,248 (2.6%) number of secondary alignments = 0 number of mapped bases = 91,248,856 bp number of sequenced bases = 89,177,503 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 639,731 duplication rate = 43.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.316 >>>>>>> ACTG content number of A's = 24,066,090 bp (26.99%) number of C's = 19,988,631 bp (22.41%) number of T's = 22,721,599 bp (25.48%) number of G's = 22,400,621 bp (25.12%) number of N's = 562 bp (0%) GC percentage = 47.53% >>>>>>> Mismatches and indels general error rate = 0.0443 number of mismatches = 3,711,017 number of insertions = 94,587 mapped reads with insertion percentage = 13.17% number of deletions = 330,905 mapped reads with deletion percentage = 45.12% homopolymer indels = 29.33% >>>>>>> Coverage mean coverageData = 0.0295X std coverageData = 8.2026X There is a 0.05% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7676018 0.030796384655747758 8.361915813272944 chr2 243199373 10848986 0.044609432442903545 14.296410059014624 chr3 198022430 2794308 0.014111068124959379 2.448319833395108 chr4 191154276 3289311 0.017207624484424297 4.294415353396913 chr5 180915260 4897158 0.02706879452844387 6.434534145884883 chr6 171115067 3373719 0.019716083797576982 3.7310223498896002 chr7 159138663 2675695 0.016813607388419496 3.2848140999672673 chr8 146364022 3370109 0.02302552877373102 4.226200389641943 chr9 141213431 4001561 0.028336971714822225 7.276880145808445 chr10 135534747 4304956 0.031762747895194725 5.137722378730461 chr11 135006516 4428652 0.032803246326273613 5.3448044552625555 chr12 133851895 4805378 0.03590070951180781 8.016984129453004 chr13 115169878 3907850 0.033931181206947186 11.764357820334356 chr14 107349540 5175006 0.04820706264786975 23.233527738901483 chr15 102531392 3117945 0.030409662242759757 5.582612684157434 chr16 90354753 1536222 0.017002116092332188 2.2613968452134863 chr17 81195210 2902888 0.03575196123022528 6.732211297779275 chr18 78077248 2755187 0.035287962506055544 8.861725666963554 chr19 59128983 2300300 0.03890308750955517 4.890001111757459 chr20 63025520 2208384 0.03503952049899787 4.866302527381731 chr21 48129895 1029112 0.02138197060267844 5.138215672134658 chr22 51304566 690257 0.013454104650256666 1.974293663238751 chrMT 16571 200530 12.101261239514814 105.07230305736067 chrX 155270560 8095205 0.05213612290700826 6.254990599602397 chrY 59373566 864119 0.014553934658396633 3.4994828365701287