BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240246.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,757,192 number of mapped reads = 1,176,152 (66.93%) number of supplementary alignments = 10,010 (0.57%) number of secondary alignments = 0 number of mapped bases = 73,551,940 bp number of sequenced bases = 73,513,852 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 220,152 duplication rate = 13.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.655 >>>>>>> ACTG content number of A's = 20,048,779 bp (27.27%) number of C's = 12,860,442 bp (17.49%) number of T's = 24,198,074 bp (32.92%) number of G's = 16,399,746 bp (22.31%) number of N's = 6,811 bp (0.01%) GC percentage = 39.8% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 658,157 number of insertions = 5,119 mapped reads with insertion percentage = 0.43% number of deletions = 22,234 mapped reads with deletion percentage = 1.87% homopolymer indels = 48.48% >>>>>>> Coverage mean coverageData = 0.0238X std coverageData = 0.3373X There is a 1.16% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% 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% 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 5285892 0.02120713673166736 0.40405413366444487 chr2 243199373 5633043 0.023162243103315897 0.34406684733998105 chr3 198022430 4506482 0.02275743207474022 0.282408818993911 chr4 191154276 4278463 0.02238225107765834 0.28962715236571845 chr5 180915260 4237599 0.023423115330348583 0.2994988597362539 chr6 171115067 4266597 0.024934081345390817 0.31712753596647797 chr7 159138663 3978090 0.024997633667438818 0.37786919378316436 chr8 146364022 3500980 0.02391967610728817 0.444992089065861 chr9 141213431 3298477 0.02335809686544618 0.3267328357771021 chr10 135534747 3734546 0.02755415922973612 0.3443087504299471 chr11 135006516 3367137 0.024940551758257358 0.31990134249164226 chr12 133851895 4415362 0.032986921851199794 0.3684780927822787 chr13 115169878 2485091 0.021577612507325917 0.29791459976366247 chr14 107349540 3045446 0.028369436888131986 0.355398883787053 chr15 102531392 2798957 0.02729853701781402 0.350111674542731 chr16 90354753 2052011 0.022710603835085465 0.291738641598141 chr17 81195210 1874261 0.023083393712510874 0.2979187208702246 chr18 78077248 1722759 0.02206480177170179 0.43607599847706746 chr19 59128983 1158006 0.019584405840364277 0.3098352893830973 chr20 63025520 2014804 0.0319680662690288 0.37273413489057433 chr21 48129895 1041092 0.021630880349936356 0.28444123589834647 chr22 51304566 747285 0.014565662635173641 0.22559574140473138 chrMT 16571 32345 1.9519039285498763 3.0439278942115298 chrX 155270560 3885175 0.025021968105222264 0.30738959552062306 chrY 59373566 192040 0.0032344360114735233 0.11095963375196824