BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080818.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 = 2,296,686 number of mapped reads = 2,044,498 (89.02%) number of supplementary alignments = 17,482 (0.76%) number of secondary alignments = 0 number of mapped bases = 137,540,828 bp number of sequenced bases = 137,487,007 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 126,614 duplication rate = 5.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3916 >>>>>>> ACTG content number of A's = 38,595,852 bp (28.07%) number of C's = 25,311,894 bp (18.41%) number of T's = 43,858,644 bp (31.9%) number of G's = 29,701,555 bp (21.6%) number of N's = 19,062 bp (0.01%) GC percentage = 40.01% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,159,878 number of insertions = 10,643 mapped reads with insertion percentage = 0.51% number of deletions = 30,506 mapped reads with deletion percentage = 1.48% homopolymer indels = 47.29% >>>>>>> Coverage mean coverageData = 0.0444X std coverageData = 0.4623X There is a 3.64% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 17996561 0.07220267266656077 1.138055371169785 chr2 243199373 8893210 0.03656756960471275 0.36011324975112735 chr3 198022430 8405817 0.04244881249058503 0.2599197911179695 chr4 191154276 8260784 0.043215271836241846 0.26819983291259175 chr5 180915260 9455504 0.052264822768405494 0.2678674785397137 chr6 171115067 9066034 0.05298209070040571 0.3045558213634903 chr7 159138663 9905582 0.0622449743718156 0.49388436717245476 chr8 146364022 6544654 0.044714909515126605 0.5284912875154205 chr9 141213431 5007257 0.03545878720275552 0.282092153258138 chr10 135534747 6340468 0.04678112543346541 0.5644452156549664 chr11 135006516 5348309 0.039615191610455305 0.27263666194877234 chr12 133851895 5286729 0.03949685583457746 0.23545521341383746 chr13 115169878 5069528 0.044017829036859794 0.24644711193828608 chr14 107349540 4195262 0.03908039102915578 0.24080448003721072 chr15 102531392 3802461 0.03708582245718463 0.22441038742813293 chr16 90354753 3461283 0.03830770252894167 0.26449291289500804 chr17 81195210 3522359 0.043381364491821624 0.2524482069190717 chr18 78077248 2191258 0.02806525660330651 0.4651251084858703 chr19 59128983 2416372 0.040866118059226554 0.7376742089745998 chr20 63025520 2982924 0.047328828068376114 0.2617012765815735 chr21 48129895 2016943 0.041906241432689596 0.26264749848790225 chr22 51304566 856604 0.016696447641716725 0.14794718797120127 chrMT 16571 12016 0.7251222014362441 1.0349333647189471 chrX 155270560 6102169 0.0393002318018303 0.2400772405082622 chrY 59373566 400740 0.006749468273473755 0.20763963742896022