BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818970.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 = 639,230 number of mapped reads = 630,105 (98.57%) number of supplementary alignments = 9,316 (1.46%) number of secondary alignments = 0 number of mapped bases = 58,344,581 bp number of sequenced bases = 58,311,939 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 167,821 duplication rate = 23.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1074 >>>>>>> ACTG content number of A's = 16,401,076 bp (28.13%) number of C's = 12,584,366 bp (21.58%) number of T's = 16,452,446 bp (28.21%) number of G's = 12,870,918 bp (22.07%) number of N's = 3,133 bp (0.01%) GC percentage = 43.65% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 358,577 number of insertions = 7,633 mapped reads with insertion percentage = 1.17% number of deletions = 17,828 mapped reads with deletion percentage = 2.77% homopolymer indels = 42.51% >>>>>>> Coverage mean coverageData = 0.0188X std coverageData = 0.2737X There is a 1.25% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 6698544 0.026874733443492605 0.5258862768245589 chr2 243199373 2849525 0.011716827082444823 0.2861291478721692 chr3 198022430 3311117 0.01672091893832431 0.1798736842241672 chr4 191154276 3404547 0.017810467394409737 0.19598086175432125 chr5 180915260 3975028 0.021971767334607373 0.20917891110811834 chr6 171115067 901355 0.005267537311603308 0.10533313013311241 chr7 159138663 3330516 0.020928389978995866 0.32395890391525217 chr8 146364022 5981972 0.040870508464163416 0.303827770179485 chr9 141213431 1385712 0.009812890956526649 0.19762260381243427 chr10 135534747 2923181 0.021567760775028415 0.29819442774085714 chr11 135006516 2201027 0.016303116806599172 0.1976917373689303 chr12 133851895 2949306 0.02203409970400494 0.20828287206643753 chr13 115169878 1357382 0.011785911590528905 0.15239434158145296 chr14 107349540 1587219 0.014785522136378041 0.17252327761544994 chr15 102531392 1284370 0.012526602584309009 0.15924156692356053 chr16 90354753 2080471 0.023025584498028565 0.29201737086388213 chr17 81195210 2139061 0.02634466983951393 0.24718845910574577 chr18 78077248 1457146 0.018662876027597693 0.2759035174902807 chr19 59128983 1362856 0.023048865900500943 0.4983364305391416 chr20 63025520 1815251 0.028801840905080988 0.24928369691890037 chr21 48129895 931435 0.019352525078228405 0.2001860681504004 chr22 51304566 525041 0.010233806480304307 0.14629936960401344 chrMT 16571 17605 1.0623981654697967 1.646250283813642 chrX 155270560 3670167 0.023637236833563297 0.2350609771956971 chrY 59373566 204747 0.0034484538119202743 0.22616763029657658