BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818866.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,854,923 number of mapped reads = 1,797,000 (96.88%) number of supplementary alignments = 29,822 (1.61%) number of secondary alignments = 0 number of mapped bases = 166,391,822 bp number of sequenced bases = 166,286,967 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 267,717 duplication rate = 11.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3313 >>>>>>> ACTG content number of A's = 45,494,963 bp (27.36%) number of C's = 36,742,541 bp (22.1%) number of T's = 48,098,208 bp (28.92%) number of G's = 35,948,620 bp (21.62%) number of N's = 2,635 bp (0%) GC percentage = 43.71% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,026,074 number of insertions = 25,740 mapped reads with insertion percentage = 1.38% number of deletions = 51,171 mapped reads with deletion percentage = 2.78% homopolymer indels = 39.7% >>>>>>> Coverage mean coverageData = 0.0537X std coverageData = 0.6549X There is a 4.1% of reference with a coverageData >= 1X There is a 0.78% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% 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 15575357 0.06248873899495721 1.0149014411840598 chr2 243199373 11872151 0.048816536216974536 0.8901813822409227 chr3 198022430 9386657 0.04740198875450624 0.2778409538478195 chr4 191154276 9091370 0.04756037997287594 0.4080926654075912 chr5 180915260 8426237 0.046575601195830575 0.2807350419247926 chr6 171115067 7520225 0.04394835084861347 0.3004612188739958 chr7 159138663 13983486 0.08786982205575021 1.2659119382456776 chr8 146364022 14859708 0.1015256877813866 0.5244138094897418 chr9 141213431 5881894 0.04165251108444493 0.5382186111847809 chr10 135534747 7727563 0.05701536448066709 1.117282860983337 chr11 135006516 7218327 0.0534665082387579 0.36611299660401775 chr12 133851895 6292130 0.04700815031419615 0.26773309243067767 chr13 115169878 3731101 0.03239650041133151 0.21735118991935062 chr14 107349540 5336940 0.04971553674100513 0.3075561143667176 chr15 102531392 4448287 0.04338463482481541 0.2527867852391652 chr16 90354753 4477681 0.04955667357089671 0.6700618208078604 chr17 81195210 5190226 0.06392281022488888 0.4305723726770615 chr18 78077248 2715695 0.03478215574401393 0.6039144249838243 chr19 59128983 3750737 0.06343313904113657 0.9816331157156797 chr20 63025520 6607736 0.10484222898914598 0.4445726441524118 chr21 48129895 2001512 0.04158562988761974 0.329937579898051 chr22 51304566 2303946 0.044907231063995356 0.2907731756517153 chrMT 16571 457959 27.636171625128235 17.818954429272452 chrX 155270560 6818977 0.04391674120322616 0.33095502374311836 chrY 59373566 715920 0.012057891217111668 0.8917841419335678