BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006191.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 8,991,720 number of mapped reads = 7,776,043 (86.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,917,317 number of mapped paired reads (second in pair) = 3,858,726 number of mapped paired reads (both in pair) = 7,185,636 number of mapped paired reads (singletons) = 590,407 number of mapped bases = 300,805,410 bp number of sequenced bases = 300,762,821 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 318,074 duplication rate = 3.45% >>>>>>> Insert size mean insert size = 54,995.7559 std insert size = 2,263,420.6673 median insert size = 101 >>>>>>> Mapping quality mean mapping quality = 47.5465 >>>>>>> ACTG content number of A's = 82,038,219 bp (27.28%) number of C's = 66,431,447 bp (22.09%) number of T's = 83,673,347 bp (27.82%) number of G's = 68,584,230 bp (22.8%) number of N's = 35,578 bp (0.01%) GC percentage = 44.89% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 963,775 number of insertions = 8,979 mapped reads with insertion percentage = 0.12% number of deletions = 31,208 mapped reads with deletion percentage = 0.4% homopolymer indels = 42.09% >>>>>>> Coverage mean coverageData = 0.0972X std coverageData = 0.5723X There is a 7.33% of reference with a coverageData >= 1X There is a 1.68% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 25632633 0.10283879292722004 0.6788404336835215 chr2 243199373 25277570 0.10393764460897685 0.48864645184203054 chr3 198022430 20130718 0.10165877673554455 0.3982658186788227 chr4 191154276 18325532 0.0958677586683962 0.42846427301054907 chr5 180915260 17847100 0.09864894757910417 0.3942986636787256 chr6 171115067 16563118 0.096795205065139 0.4278596257742053 chr7 159138663 16380182 0.102930247692228 0.5795188756724341 chr8 146364022 15044367 0.10278732979884907 1.0864564919138122 chr9 141213431 11569905 0.08193204370199036 0.41605248920010746 chr10 135534747 14428125 0.10645332890170223 0.5399097040939279 chr11 135006516 13349102 0.09887746455141469 0.47521349895760207 chr12 133851895 13582694 0.1014755450417792 0.403815648445145 chr13 115169878 9302328 0.08077049452114554 0.360825499166127 chr14 107349540 9320991 0.08682842050371152 1.3289529444710562 chr15 102531392 9179189 0.08952564498490374 0.3771801945935788 chr16 90354753 9699928 0.10735382122067226 0.47251173287499953 chr17 81195210 8836865 0.10883480688084925 0.4402721972541204 chr18 78077248 7574139 0.09700827313995493 0.6513337227528443 chr19 59128983 6764112 0.11439587925941497 0.5803158460060802 chr20 63025520 6340378 0.10060016958209944 0.4277643373544833 chr21 48129895 4010424 0.08332501037037375 0.42963947353766946 chr22 51304566 4184417 0.08156032350025141 0.4154836229569164 chrMT 16571 6257 0.3775873513970189 0.7788444349005378 chrX 155270560 16706904 0.10759865875411283 0.4390103742687391 chrY 59373566 748432 0.012605474968439659 0.27563416585442696