BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006019.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 = 11,148,626 number of mapped reads = 8,196,723 (73.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,125,727 number of mapped paired reads (second in pair) = 4,070,996 number of mapped paired reads (both in pair) = 7,433,808 number of mapped paired reads (singletons) = 762,915 number of mapped bases = 316,525,570 bp number of sequenced bases = 316,487,344 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 283,027 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 60,190.2434 std insert size = 2,380,532.9805 median insert size = 72 >>>>>>> Mapping quality mean mapping quality = 46.6811 >>>>>>> ACTG content number of A's = 90,124,430 bp (28.48%) number of C's = 66,920,987 bp (21.14%) number of T's = 91,412,469 bp (28.88%) number of G's = 67,986,452 bp (21.48%) number of N's = 43,006 bp (0.01%) GC percentage = 42.63% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 1,628,572 number of insertions = 9,870 mapped reads with insertion percentage = 0.12% number of deletions = 29,838 mapped reads with deletion percentage = 0.36% homopolymer indels = 44.75% >>>>>>> Coverage mean coverageData = 0.1022X std coverageData = 0.5498X There is a 7.36% of reference with a coverageData >= 1X There is a 2.08% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.14% 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% 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 25282086 0.10143238920957393 0.745845195611142 chr2 243199373 27069921 0.11130752791866778 0.546001752974421 chr3 198022430 22240511 0.11231308998682624 0.42971119699872423 chr4 191154276 21118010 0.11047626263929351 0.47888436280352603 chr5 180915260 19350309 0.10695785971841182 0.4195058472148888 chr6 171115067 18638856 0.10892586098218926 0.607589326457307 chr7 159138663 17150313 0.10776961849930837 0.67578275429893 chr8 146364022 16173759 0.11050365232515953 0.9251275037833482 chr9 141213431 13269499 0.09396768356970238 0.4648910788592497 chr10 135534747 14716528 0.10858121865974339 0.6246185564068315 chr11 135006516 14537849 0.10768257289151881 0.48698570997814944 chr12 133851895 14325764 0.10702697933413644 0.4225888527080531 chr13 115169878 10039221 0.08716880814964482 0.37804413236115386 chr14 107349540 9892407 0.09215136832444741 0.4127602479861166 chr15 102531392 9284277 0.0905505798653353 0.3884131050378525 chr16 90354753 9175436 0.10154901314378005 0.4669578855890401 chr17 81195210 7975831 0.09823031432519233 0.4138605373850947 chr18 78077248 7881732 0.10094787152334057 0.6554726917850767 chr19 59128983 6312102 0.10675140480599844 0.7003617892466317 chr20 63025520 6312104 0.10015155765474049 0.4254276718309432 chr21 48129895 4020956 0.08354383486604323 0.42289232992656756 chr22 51304566 3543680 0.06907143508435487 0.36748797520323123 chrMT 16571 28543 1.722466960352423 2.205444058309428 chrX 155270560 17393145 0.11201830533747029 0.4621473351219822 chrY 59373566 792731 0.013351581409140896 0.28167649580844584