BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085013.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 = 2,312,233 number of mapped reads = 2,093,982 (90.56%) number of supplementary alignments = 12,335 (0.53%) number of secondary alignments = 0 number of mapped bases = 140,725,010 bp number of sequenced bases = 140,672,172 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,474 duplication rate = 2.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8392 >>>>>>> ACTG content number of A's = 38,633,323 bp (27.46%) number of C's = 27,827,827 bp (19.78%) number of T's = 42,615,532 bp (30.29%) number of G's = 31,579,660 bp (22.45%) number of N's = 15,830 bp (0.01%) GC percentage = 42.23% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,254,287 number of insertions = 9,120 mapped reads with insertion percentage = 0.43% number of deletions = 29,577 mapped reads with deletion percentage = 1.4% homopolymer indels = 47.7% >>>>>>> Coverage mean coverageData = 0.0455X std coverageData = 0.301X There is a 3.9% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 12412315 0.04979853189613517 0.3962922482297292 chr2 243199373 13525460 0.05561469930269927 0.3684933071619933 chr3 198022430 8546463 0.04315906536446402 0.233849776731842 chr4 191154276 7837110 0.04099887360092327 0.23341694599208782 chr5 180915260 6915631 0.03822580251107618 0.21945425948304373 chr6 171115067 9368743 0.05475112837375098 0.33075419477370166 chr7 159138663 12357995 0.07765551605771628 0.372958630864937 chr8 146364022 8313933 0.05680311928022858 0.40187104662023876 chr9 141213431 5087408 0.03602637485665227 0.2895861430817959 chr10 135534747 10116585 0.07464200305771036 0.37196434483429325 chr11 135006516 5850784 0.04333704900584206 0.33841244334430487 chr12 133851895 5820662 0.043485839330104366 0.24002935120757785 chr13 115169878 2760202 0.023966353424460518 0.17174993818932105 chr14 107349540 4713782 0.04391059337562136 0.24687197038320616 chr15 102531392 2404419 0.02345056429156838 0.17770798633561227 chr16 90354753 4089134 0.0452564349326482 0.24611933349795023 chr17 81195210 2403673 0.029603630558994797 0.21213029796971916 chr18 78077248 3352434 0.04293739963785609 0.42818882934246283 chr19 59128983 2435135 0.04118344129138835 0.29517088211824766 chr20 63025520 3369101 0.053456139671675854 0.2628539089798242 chr21 48129895 1628045 0.033826065899375014 0.21981100051940264 chr22 51304566 1090416 0.021253780803837226 0.16158037005327716 chrMT 16571 15736 0.9496107657956672 1.1128368292716222 chrX 155270560 6040425 0.03890257753948978 0.24087700280324914 chrY 59373566 269419 0.004537692750339436 0.09525724105025404