BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548962.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,482,376 number of mapped reads = 7,424,678 (87.53%) number of secondary alignments = 0 number of mapped bases = 293,063,672 bp number of sequenced bases = 293,034,229 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 390,213 duplication rate = 2.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 34.2857 >>>>>>> ACTG content number of A's = 82,025,430 bp (27.99%) number of C's = 63,526,054 bp (21.68%) number of T's = 83,704,748 bp (28.56%) number of G's = 63,777,615 bp (21.76%) number of N's = 382 bp (0%) GC percentage = 43.44% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 1,018,877 number of insertions = 11,147 mapped reads with insertion percentage = 0.15% number of deletions = 23,147 mapped reads with deletion percentage = 0.31% homopolymer indels = 37.34% >>>>>>> Coverage mean coverageData = 0.0947X std coverageData = 1.1361X There is a 7.79% of reference with a coverageData >= 1X There is a 1.1% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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% 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 23533012 0.09441505864894113 2.125455825930275 chr2 243199373 25029858 0.10291908935143512 1.081033282195882 chr3 198022430 19766145 0.09981770751929465 0.37894005641358625 chr4 191154276 19185749 0.1003678777240641 0.42895304051866046 chr5 180915260 18070575 0.09988419440129041 0.413289197164012 chr6 171115067 17066718 0.09973825390840656 0.425874066992611 chr7 159138663 17120547 0.10758257407252442 1.9129356405097122 chr8 146364022 15252559 0.1042097558647302 2.0708677973805356 chr9 141213431 12545030 0.08883737128375559 1.1439720769945818 chr10 135534747 13936029 0.10282255516365851 0.8298142481109609 chr11 135006516 13552271 0.10038234747128798 0.7675906998379761 chr12 133851895 13560251 0.10130787464757222 0.4548020537872139 chr13 115169878 9148618 0.07943585735152034 0.3184345543280397 chr14 107349540 8973372 0.08359022311600031 0.6310735253530784 chr15 102531392 8172631 0.07970857354594386 0.347190821860691 chr16 90354753 8211654 0.09088236896624576 0.528432913370077 chr17 81195210 7966260 0.09811243791351731 0.418108231747343 chr18 78077248 7882919 0.1009630744157376 2.2103263800708324 chr19 59128983 6817338 0.1152960469487527 2.128760436446677 chr20 63025520 5892769 0.09349814170513786 0.4192430574676784 chr21 48129895 3680794 0.07647625244143998 0.5672271298447523 chr22 51304566 3337350 0.06504976574599618 0.5084848961488777 chrMT 16571 9390 0.5666525858427374 1.013018438099494 chrX 155270560 11606009 0.07474700290898674 0.614465470841712 chrY 59373566 2745824 0.04624657376988271 0.4158111021568559