BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085126.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,051,045 number of mapped reads = 1,824,738 (88.97%) number of supplementary alignments = 15,561 (0.76%) number of secondary alignments = 0 number of mapped bases = 121,751,766 bp number of sequenced bases = 121,707,988 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,359 duplication rate = 2.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6413 >>>>>>> ACTG content number of A's = 33,917,648 bp (27.87%) number of C's = 22,533,089 bp (18.51%) number of T's = 38,150,918 bp (31.35%) number of G's = 27,084,071 bp (22.25%) number of N's = 22,262 bp (0.02%) GC percentage = 40.77% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,078,661 number of insertions = 9,644 mapped reads with insertion percentage = 0.52% number of deletions = 27,102 mapped reads with deletion percentage = 1.47% homopolymer indels = 46.58% >>>>>>> Coverage mean coverageData = 0.0393X std coverageData = 0.3339X There is a 3.51% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 9792363 0.039287216058731506 0.5611169066400784 chr2 243199373 10414336 0.04282221566418266 0.40661098833719217 chr3 198022430 8351531 0.042174671828842825 0.2229401878550017 chr4 191154276 8264813 0.04323634905242716 0.23399493255378553 chr5 180915260 7706160 0.04259541179666104 0.22490755493569284 chr6 171115067 7039111 0.0411367106556432 0.25919330247226996 chr7 159138663 6070093 0.03814342087315387 0.4032458450207051 chr8 146364022 6371123 0.04352929711100724 0.5651310375618305 chr9 141213431 5091483 0.03605523188513138 0.2925526934456889 chr10 135534747 5641167 0.04162155554103038 0.30112776397423796 chr11 135006516 5514435 0.04084569518111259 0.28328204582832395 chr12 133851895 5532814 0.04133534306705183 0.22415001087358244 chr13 115169878 4109652 0.03568339283992295 0.20699569874452153 chr14 107349540 3764133 0.03506426762518032 0.21679488543915154 chr15 102531392 3374955 0.03291630918265501 0.20493286256339904 chr16 90354753 3253268 0.03600549934545225 0.2228353047172853 chr17 81195210 3119898 0.038424655838688024 0.22860579209079956 chr18 78077248 3309895 0.04239256742245833 0.4891734469883679 chr19 59128983 2273686 0.038452986752706364 0.4479941040721032 chr20 63025520 2432536 0.03859604807703292 0.21767105160176106 chr21 48129895 1610495 0.033461427663617385 0.20818527037076617 chr22 51304566 1289719 0.025138483775498658 0.17163072092094644 chrMT 16571 2445 0.14754691931687888 0.4106370192612052 chrX 155270560 7120965 0.045861655937867424 0.25427514636274895 chrY 59373566 300690 0.005064374944230232 0.10778773413435949