BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818946.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 = 2,699,253 number of mapped reads = 2,659,423 (98.52%) number of supplementary alignments = 33,755 (1.25%) number of secondary alignments = 0 number of mapped bases = 246,356,553 bp number of sequenced bases = 246,222,067 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,198,277 duplication rate = 38.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2909 >>>>>>> ACTG content number of A's = 71,868,667 bp (29.19%) number of C's = 53,113,474 bp (21.57%) number of T's = 69,510,973 bp (28.23%) number of G's = 51,717,906 bp (21%) number of N's = 11,047 bp (0%) GC percentage = 42.58% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,571,124 number of insertions = 30,790 mapped reads with insertion percentage = 1.13% number of deletions = 74,583 mapped reads with deletion percentage = 2.75% homopolymer indels = 43.04% >>>>>>> Coverage mean coverageData = 0.0796X std coverageData = 0.8389X There is a 3.53% of reference with a coverageData >= 1X There is a 1.8% of reference with a coverageData >= 2X There is a 1.01% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.34% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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% 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 29250850 0.11735517401178311 1.4354114705035204 chr2 243199373 21575314 0.08871451325657817 1.2192384918545005 chr3 198022430 16833741 0.08500926384955482 0.5502093272663587 chr4 191154276 15921537 0.08329155556007546 0.6022593138423414 chr5 180915260 12744733 0.07044587062473337 0.5232727132153232 chr6 171115067 12949343 0.07567622902546624 0.5763367361732289 chr7 159138663 12378099 0.07778184613754106 0.6990799521635583 chr8 146364022 16276898 0.11120832686601083 0.7473291080323494 chr9 141213431 9306479 0.0659036391517178 0.9782678723364292 chr10 135534747 12248162 0.09036916562805847 1.0607899240773857 chr11 135006516 9421124 0.06978273552366909 0.600553188365115 chr12 133851895 11076202 0.08274968389502442 0.5498919604837007 chr13 115169878 3929709 0.034120979098371536 0.34280491110446865 chr14 107349540 5677797 0.05289074363988891 0.4893118196784191 chr15 102531392 7173639 0.0699652941413299 0.5007511309133552 chr16 90354753 7370870 0.08157700348093476 0.8686858286728518 chr17 81195210 5247190 0.06462437870411321 0.5406451958730925 chr18 78077248 6222545 0.07969728902330164 1.1802975301099643 chr19 59128983 3861322 0.0653033724594925 1.2179032214072154 chr20 63025520 5308123 0.08422180411998187 0.587650698492342 chr21 48129895 3243695 0.06739459955190012 0.5511979631293914 chr22 51304566 2994655 0.05837014584627809 0.5045374930337135 chrMT 16571 451137 27.224488564359422 16.677532678639288 chrX 155270560 14178605 0.09131547538696325 0.7051489844886036 chrY 59373566 714784 0.0120387581234383 0.7488441678159147