BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504745.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 1,843,854 number of mapped reads = 1,680,648 (91.15%) number of secondary alignments = 0 number of mapped bases = 53,775,528 bp number of sequenced bases = 53,775,528 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 150,164 duplication rate = 6.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 6.3144 >>>>>>> ACTG content number of A's = 15,403,365 bp (28.64%) number of C's = 10,913,771 bp (20.3%) number of T's = 16,334,109 bp (30.37%) number of G's = 11,123,940 bp (20.69%) number of N's = 343 bp (0%) GC percentage = 40.98% >>>>>>> Mismatches and indels general error rate = 0.0005 number of mismatches = 24,717 >>>>>>> Coverage mean coverageData = 0.0174X std coverageData = 0.3911X There is a 1.05% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 2831506 0.011360076009599993 0.3435238277525477 chr2 243199373 5776470 0.02375199380139849 0.2411441152002727 chr3 198022430 2390272 0.012070713403527064 0.3070752603276461 chr4 191154276 1221810 0.00639174820237869 0.15099542422665627 chr5 180915260 3119154 0.01724096684823602 0.4074344461316761 chr6 171115067 1847268 0.010795472499215981 0.22198397979073264 chr7 159138663 4145364 0.026048754726561953 0.6771594352471768 chr8 146364022 1317070 0.008998591197500709 0.22778091575573747 chr9 141213431 2644120 0.018724281261886484 0.22085020590521057 chr10 135534747 3549710 0.026190405623437656 0.27601837490753256 chr11 135006516 2284556 0.016921820277178326 0.8709307946938074 chr12 133851895 4251278 0.031761059490416625 0.3302411955094219 chr13 115169878 364676 0.0031664182191805394 0.09620607225868646 chr14 107349540 363236 0.003383675421431708 0.07058787144200969 chr15 102531392 2256840 0.022011209991180065 0.28900792774617096 chr16 90354753 803430 0.008891950598326577 0.24611190254841947 chr17 81195210 548998 0.006761457972705533 0.11489099571641508 chr18 78077248 1526762 0.019554505814549202 0.444862487266949 chr19 59128983 978718 0.01655225492378247 0.3063099703239699 chr20 63025520 1691100 0.026831988058170723 0.42483088218330434 chr21 48129895 709028 0.014731550941467875 0.16242357840824373 chr22 51304566 533718 0.010402933727185218 0.1514112359585991 chrMT 16571 64 0.003862168849194376 0.062026224300489936 chrX 155270560 8402914 0.05411788300370656 0.8077512948553611 chrY 59373566 217466 0.0036626737225114625 0.0786612581435251