BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054611.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 = 17,350,656 number of mapped reads = 13,119,903 (75.62%) number of supplementary alignments = 344 (0%) number of secondary alignments = 0 number of mapped bases = 621,996,563 bp number of sequenced bases = 621,869,059 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,882,277 duplication rate = 20.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6051 >>>>>>> ACTG content number of A's = 186,687,983 bp (30.02%) number of C's = 113,256,400 bp (18.21%) number of T's = 195,019,596 bp (31.36%) number of G's = 126,902,114 bp (20.41%) number of N's = 2,966 bp (0%) GC percentage = 38.62% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 3,185,923 number of insertions = 25,022 mapped reads with insertion percentage = 0.19% number of deletions = 85,857 mapped reads with deletion percentage = 0.65% homopolymer indels = 49.56% >>>>>>> Coverage mean coverageData = 0.2009X std coverageData = 1.5678X There is a 6.38% of reference with a coverageData >= 1X There is a 3.22% of reference with a coverageData >= 2X There is a 2.08% of reference with a coverageData >= 3X There is a 1.48% of reference with a coverageData >= 4X There is a 1.11% of reference with a coverageData >= 5X There is a 0.86% of reference with a coverageData >= 6X There is a 0.68% of reference with a coverageData >= 7X There is a 0.55% of reference with a coverageData >= 8X There is a 0.45% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.27% 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 0.17% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% 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 0.02% of reference with a coverageData >= 34X There is a 0.02% 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 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 57885583 0.2322384705312329 1.781357809128237 chr2 243199373 46401681 0.1907968775889895 1.6827719404718073 chr3 198022430 49304270 0.2489832591186766 1.657808093345065 chr4 191154276 39951122 0.20899936342517392 1.5393785439692924 chr5 180915260 32364052 0.17889066958751848 1.3210911114064918 chr6 171115067 31336409 0.1831306240262291 1.4317729753115516 chr7 159138663 38562117 0.2423177138292283 1.735316734515795 chr8 146364022 33935989 0.23186018350875873 1.698022312702221 chr9 141213431 29745918 0.21064510499713018 1.603682779778478 chr10 135534747 27028054 0.19941789539770197 1.6366228763782729 chr11 135006516 28752449 0.2129708243119169 1.5673100120869152 chr12 133851895 22926082 0.17127947273365088 1.2769592401666499 chr13 115169878 12675735 0.11006120020375466 1.005230030628745 chr14 107349540 15456010 0.14397835333062442 1.3540384608847293 chr15 102531392 16039921 0.15643912256648188 1.2103147522764204 chr16 90354753 16231819 0.17964543602924796 1.4873527757326173 chr17 81195210 10231519 0.12601136200029533 1.0325299347114127 chr18 78077248 24148978 0.3092959680136267 2.24409591120558 chr19 59128983 10257978 0.17348476972790147 1.4809473683345091 chr20 63025520 9347554 0.14831379415830287 1.2545214866685237 chr21 48129895 8354075 0.173573513925181 1.5330037260706244 chr22 51304566 6969883 0.13585307397396168 1.1182547230830164 chrMT 16571 68489 4.1330637861324 9.822005686403507 chrX 155270560 52095458 0.33551407298331376 2.1164137538447103 chrY 59373566 1925418 0.03242887584013397 0.7463192241520062