BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054568.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 14,437,964 number of mapped reads = 10,664,492 (73.86%) number of supplementary alignments = 276 (0%) number of secondary alignments = 0 number of mapped bases = 503,337,133 bp number of sequenced bases = 503,230,686 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,677,445 duplication rate = 22.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6479 >>>>>>> ACTG content number of A's = 152,393,210 bp (30.28%) number of C's = 98,177,327 bp (19.51%) number of T's = 148,641,740 bp (29.54%) number of G's = 103,896,276 bp (20.65%) number of N's = 122,133 bp (0.02%) GC percentage = 40.16% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 2,786,499 number of insertions = 22,603 mapped reads with insertion percentage = 0.21% number of deletions = 71,367 mapped reads with deletion percentage = 0.67% homopolymer indels = 47.45% >>>>>>> Coverage mean coverageData = 0.1626X std coverageData = 1.4829X There is a 4.75% of reference with a coverageData >= 1X There is a 2.31% of reference with a coverageData >= 2X There is a 1.55% of reference with a coverageData >= 3X There is a 1.15% of reference with a coverageData >= 4X There is a 0.9% of reference with a coverageData >= 5X There is a 0.72% of reference with a coverageData >= 6X There is a 0.59% of reference with a coverageData >= 7X There is a 0.49% of reference with a coverageData >= 8X There is a 0.41% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.23% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 41499950 0.16649888306597238 1.5429340370288092 chr2 243199373 54529387 0.22421680749974632 1.7909973041999991 chr3 198022430 32700599 0.1651358333497877 1.4545210642014175 chr4 191154276 24220717 0.12670769133095405 1.2819406740812995 chr5 180915260 24818423 0.13718258481899206 1.2653678052646338 chr6 171115067 30929176 0.1807507459293459 1.5912033724885368 chr7 159138663 26383721 0.1657907670117852 1.5427023859630773 chr8 146364022 27720907 0.18939700222230843 1.6411632065424677 chr9 141213431 26197856 0.18551957710028305 1.5895477786190186 chr10 135534747 17185998 0.12680141720410634 1.274638348007272 chr11 135006516 23781616 0.17615161626717335 1.5157708938143064 chr12 133851895 26499496 0.19797624830040694 1.605907016471224 chr13 115169878 13641585 0.11844750760263895 1.1952355690457512 chr14 107349540 9723539 0.09057830149994121 1.0956996073141816 chr15 102531392 14611499 0.14250756490265928 1.3045938396297727 chr16 90354753 12061737 0.13349311020749513 1.2804763922209723 chr17 81195210 11488160 0.1414881493625055 1.29523271022581 chr18 78077248 15512459 0.19868091406090543 1.7551248248570916 chr19 59128983 10199091 0.1724888621879392 1.5439062436779571 chr20 63025520 10757921 0.17069150718629533 1.490664518711567 chr21 48129895 5521118 0.11471286193331608 1.2810577188941221 chr22 51304566 8811538 0.1717495865767581 1.5218130229168296 chrMT 16571 65492 3.9522056604912197 8.041730260366723 chrX 155270560 33282806 0.21435361603642056 1.763398203037107 chrY 59373566 1192342 0.020082034486525537 0.4478522668298609