BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548992.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 5,757,062 number of mapped reads = 4,969,522 (86.32%) number of secondary alignments = 0 number of mapped bases = 197,310,548 bp number of sequenced bases = 197,289,201 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 295,985 duplication rate = 5.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1734 >>>>>>> ACTG content number of A's = 60,351,001 bp (30.59%) number of C's = 38,361,518 bp (19.44%) number of T's = 59,184,546 bp (30%) number of G's = 39,390,598 bp (19.97%) number of N's = 1,538 bp (0%) GC percentage = 39.41% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 613,097 number of insertions = 5,681 mapped reads with insertion percentage = 0.11% number of deletions = 16,546 mapped reads with deletion percentage = 0.33% homopolymer indels = 43.41% >>>>>>> Coverage mean coverageData = 0.0637X std coverageData = 0.5245X There is a 5.29% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 15887346 0.06374044700975891 0.8005503391790246 chr2 243199373 17190504 0.07068482039219731 0.39950924382404357 chr3 198022430 14179733 0.07160670132166341 0.31055683644896803 chr4 191154276 13965027 0.07305631499449168 0.33163148463107195 chr5 180915260 12961716 0.07164523324345332 0.3143328046792771 chr6 171115067 12176230 0.07115814062124641 0.34877360291151244 chr7 159138663 10871966 0.06831756529210001 0.5546463664816305 chr8 146364022 10567365 0.07219919796956659 1.4471030297896936 chr9 141213431 8344902 0.05909425145261147 0.366438939485483 chr10 135534747 9278226 0.06845643796420707 0.4257301644708336 chr11 135006516 9000285 0.06666556005341254 0.3730231013995353 chr12 133851895 9244980 0.06906872704342362 0.3156794081337248 chr13 115169878 6780856 0.058876992124624807 0.2790154799374446 chr14 107349540 6176636 0.05753761031486488 0.3343389956701472 chr15 102531392 5524490 0.05388096164733626 0.26693709170394786 chr16 90354753 5136588 0.056849117832240656 0.3067255529060971 chr17 81195210 4646103 0.057221392739793396 0.3020891154917776 chr18 78077248 5460610 0.06993855623599848 0.7383360781542172 chr19 59128983 3149945 0.05327243663230264 0.627737021760035 chr20 63025520 3821718 0.06063762742457341 0.30198435784424277 chr21 48129895 2611766 0.054264942817764304 0.31853064059528796 chr22 51304566 1856836 0.036192412191928494 0.23284176624406777 chrMT 16571 13236 0.7987447951240119 1.3146517900391266 chrX 155270560 6713078 0.04323471236272993 0.2925968716126486 chrY 59373566 1750406 0.02948123412361656 0.31957160770926196