BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818948.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 4,252,339 number of mapped reads = 4,185,734 (98.43%) number of supplementary alignments = 51,884 (1.22%) number of secondary alignments = 0 number of mapped bases = 388,353,284 bp number of sequenced bases = 388,136,415 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,359,831 duplication rate = 45.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.262 >>>>>>> ACTG content number of A's = 108,762,574 bp (28.02%) number of C's = 81,647,817 bp (21.04%) number of T's = 111,215,192 bp (28.65%) number of G's = 86,494,857 bp (22.28%) number of N's = 15,975 bp (0%) GC percentage = 43.32% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 2,406,785 number of insertions = 51,189 mapped reads with insertion percentage = 1.19% number of deletions = 118,673 mapped reads with deletion percentage = 2.78% homopolymer indels = 42.07% >>>>>>> Coverage mean coverageData = 0.1254X std coverageData = 1.3408X There is a 4.3% of reference with a coverageData >= 1X There is a 2.49% of reference with a coverageData >= 2X There is a 1.64% of reference with a coverageData >= 3X There is a 1.12% of reference with a coverageData >= 4X There is a 0.77% of reference with a coverageData >= 5X There is a 0.54% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% 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% 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 44986467 0.18048688031152388 2.428408419436238 chr2 243199373 33673517 0.1384605420014796 1.9204642696521226 chr3 198022430 25969792 0.13114570909972167 0.8259392435143158 chr4 191154276 24838582 0.12993997581304434 0.9451157623344856 chr5 180915260 19902726 0.11001131690052017 0.7846342922746944 chr6 171115067 20822739 0.12168851852186692 0.8965432473370456 chr7 159138663 19903095 0.1250676273433314 1.0410130564447422 chr8 146364022 25691345 0.17553046608680922 1.14105527702997 chr9 141213431 14566658 0.10315348828256996 1.5296936028168466 chr10 135534747 18838066 0.13899067521039457 1.6673191236969516 chr11 135006516 14694404 0.10884218358764254 0.9144589409837388 chr12 133851895 17715742 0.132353314833533 0.8506537979605094 chr13 115169878 6336833 0.05502161771848017 0.5223211458524547 chr14 107349540 9488017 0.08838432842842177 0.7946338970125709 chr15 102531392 11564619 0.11279100746042733 0.7869449253203638 chr16 90354753 11912414 0.13184047993579265 1.4190211766142315 chr17 81195210 8510864 0.10481977939339032 0.8631364405549622 chr18 78077248 9769912 0.12513135708881543 1.8510864317513807 chr19 59128983 6268091 0.10600708285478207 2.2002951494531375 chr20 63025520 8866226 0.14067676077880834 0.9403534568793454 chr21 48129895 5279562 0.10969402696598445 0.8659811345103063 chr22 51304566 4926055 0.09601591795942685 0.8032621072037842 chrMT 16571 587136 35.431537022509204 22.97672629837188 chrX 155270560 22061780 0.14208604644692466 1.0276437304674109 chrY 59373566 1178642 0.01985129207162662 1.1874795857374965