BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083663.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 = 1,929,301 number of mapped reads = 1,548,722 (80.27%) number of supplementary alignments = 10,849 (0.56%) number of secondary alignments = 0 number of mapped bases = 95,640,259 bp number of sequenced bases = 95,608,145 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,475 duplication rate = 2.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4236 >>>>>>> ACTG content number of A's = 28,373,333 bp (29.68%) number of C's = 18,245,431 bp (19.08%) number of T's = 28,471,414 bp (29.78%) number of G's = 20,512,118 bp (21.45%) number of N's = 5,849 bp (0.01%) GC percentage = 40.54% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 811,633 number of insertions = 7,042 mapped reads with insertion percentage = 0.45% number of deletions = 19,921 mapped reads with deletion percentage = 1.27% homopolymer indels = 46.41% >>>>>>> Coverage mean coverageData = 0.0309X std coverageData = 0.2969X There is a 2.78% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% 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 8729155 0.035021597799750316 0.6992711013518457 chr2 243199373 8107688 0.03333761884328542 0.23094701274198667 chr3 198022430 8552083 0.043187445987810574 0.22707446947539417 chr4 191154276 5209701 0.027253907728436062 0.18006529801298451 chr5 180915260 5010312 0.02769424757204008 0.18047034990205432 chr6 171115067 8110268 0.04739657437646914 0.272510914057907 chr7 159138663 5694457 0.03578298882654305 0.3391219367215725 chr8 146364022 5996547 0.040970088947132104 0.33868800439554914 chr9 141213431 5242227 0.03712272241299767 0.22788849632344735 chr10 135534747 4551475 0.03358160988783194 0.2803720836855111 chr11 135006516 2606263 0.019304720077362784 0.16554561664571385 chr12 133851895 3580421 0.026749124470744325 0.1764653164028469 chr13 115169878 3145769 0.027314164559590834 0.17807408492896268 chr14 107349540 2008487 0.018709786739654403 0.14896465316265406 chr15 102531392 2343663 0.022858004307597813 0.16408377380318948 chr16 90354753 2261614 0.025030382186978034 0.17604976235193026 chr17 81195210 1992370 0.024538023856333396 0.1708409457805423 chr18 78077248 3020850 0.03869052864158327 0.3136847373530149 chr19 59128983 2431681 0.04112502662188525 0.43913586470486904 chr20 63025520 1437828 0.02281342541878274 0.16352581289896556 chr21 48129895 1728453 0.035912253704272576 0.20703978478133048 chr22 51304566 617894 0.01204364539405713 0.11723594966866485 chrMT 16571 11702 0.7061734355198841 0.946484034819414 chrX 155270560 3076167 0.019811656504620065 0.15855470402964056 chrY 59373566 173184 0.002916853604514844 0.07244725878305071