BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926974.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 20,605,450 number of mapped reads = 20,327,915 (98.65%) number of supplementary alignments = 155,289 (0.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,205,251 number of mapped paired reads (second in pair) = 10,122,664 number of mapped paired reads (both in pair) = 20,171,116 number of mapped paired reads (singletons) = 156,799 number of mapped bases = 1,952,434,096 bp number of sequenced bases = 1,950,959,417 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,058,661 duplication rate = 3.9% >>>>>>> Insert size mean insert size = 80,731.4157 std insert size = 2,803,144.9858 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 53.659 >>>>>>> ACTG content number of A's = 561,376,467 bp (28.77%) number of C's = 394,308,775 bp (20.21%) number of T's = 567,225,806 bp (29.07%) number of G's = 427,889,401 bp (21.93%) number of N's = 158,968 bp (0.01%) GC percentage = 42.14% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 18,535,168 number of insertions = 315,380 mapped reads with insertion percentage = 1.53% number of deletions = 1,043,801 mapped reads with deletion percentage = 5% homopolymer indels = 53.15% >>>>>>> Coverage mean coverageData = 0.6307X std coverageData = 2.6626X There is a 27.96% of reference with a coverageData >= 1X There is a 14.62% of reference with a coverageData >= 2X There is a 7.79% of reference with a coverageData >= 3X There is a 4.46% of reference with a coverageData >= 4X There is a 2.64% of reference with a coverageData >= 5X There is a 1.61% of reference with a coverageData >= 6X There is a 1% of reference with a coverageData >= 7X There is a 0.64% of reference with a coverageData >= 8X There is a 0.41% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% 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 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 160283813 0.6430628431613817 3.205281034885394 chr2 243199373 169653354 0.6975896027495104 4.13215713747384 chr3 198022430 130442819 0.658727493648068 1.4359855641454196 chr4 191154276 115900255 0.6063178780264377 1.9584012247177949 chr5 180915260 118004880 0.65226603880734 1.4064397156614439 chr6 171115067 113339772 0.6623599779205884 2.4268020148582052 chr7 159138663 102381410 0.6433471795600042 2.0198128942486644 chr8 146364022 99622555 0.6806492035317259 1.706200432194324 chr9 141213431 84083719 0.5954371224079953 3.64466664760175 chr10 135534747 93372313 0.6889178979321074 3.963373343897663 chr11 135006516 92593856 0.6858473112512584 2.4733287448755092 chr12 133851895 85871645 0.6415422433877384 1.657884119968873 chr13 115169878 58330160 0.5064706242026236 1.3197143790188426 chr14 107349540 59042030 0.5499979785660936 1.36287927321573 chr15 102531392 58773196 0.5732214773793376 1.4301681045976924 chr16 90354753 65759512 0.727792504728556 5.570548465111259 chr17 81195210 51064191 0.6289064465748657 2.466583126090001 chr18 78077248 52748410 0.6755925874846409 3.8694367942393972 chr19 59128983 31181053 0.5273395789675598 2.1540327094059624 chr20 63025520 45751492 0.7259201034755445 1.6192497139976918 chr21 48129895 23998287 0.4986149876287908 1.8935943467735679 chr22 51304566 25163258 0.49046819731405583 1.3370115016713366 chrMT 16571 30406 1.8348922816969404 2.0099568632667184 chrX 155270560 111814038 0.7201238792466518 1.748674987607184 chrY 59373566 3227672 0.05436210450960618 1.6767920476229623