BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054597.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 = 3,261,041 number of mapped reads = 2,583,187 (79.21%) number of supplementary alignments = 103 (0%) number of secondary alignments = 0 number of mapped bases = 121,757,230 bp number of sequenced bases = 121,732,172 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 296,087 duplication rate = 9.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7007 >>>>>>> ACTG content number of A's = 36,095,619 bp (29.65%) number of C's = 23,645,955 bp (19.42%) number of T's = 36,518,341 bp (30%) number of G's = 25,471,263 bp (20.92%) number of N's = 994 bp (0%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 897,468 number of insertions = 5,228 mapped reads with insertion percentage = 0.2% number of deletions = 17,118 mapped reads with deletion percentage = 0.66% homopolymer indels = 46.02% >>>>>>> Coverage mean coverageData = 0.0393X std coverageData = 0.3348X There is a 2.55% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% 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% 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 11400914 0.04574076467396244 0.3766284787024304 chr2 243199373 9624284 0.039573638209996535 0.39687403142639127 chr3 198022430 9188837 0.04640301101243935 0.34845812608807536 chr4 191154276 7880945 0.041228190992703716 0.33388787198360037 chr5 180915260 6091744 0.03367180855832725 0.2796777522172526 chr6 171115067 5908189 0.03452757903545688 0.304114163899052 chr7 159138663 8184780 0.05143175043515352 0.39795018989682884 chr8 146364022 7462032 0.05098269300087968 0.38057728520521805 chr9 141213431 5694148 0.04032299165650893 0.33261715789167456 chr10 135534747 5376419 0.03966819667284287 0.32761108091608987 chr11 135006516 5541342 0.04104499667260505 0.33446021967123607 chr12 133851895 4554624 0.034027340442210396 0.28461711953279856 chr13 115169878 3977649 0.034537233772184775 0.29135466505120156 chr14 107349540 2819560 0.02626522666049617 0.2840923324830667 chr15 102531392 2909727 0.02837888907233406 0.2559345102084787 chr16 90354753 3223038 0.03567092923158121 0.31206191456664734 chr17 81195210 2186319 0.026926699247406344 0.24513326828009807 chr18 78077248 4574383 0.05858791283217359 0.4209780671731128 chr19 59128983 2317403 0.039192336523021204 0.3577668014480689 chr20 63025520 2105406 0.033405610933475834 0.28912817147638026 chr21 48129895 1512983 0.0314354103618967 0.3125548849985927 chr22 51304566 1316189 0.025654422259414493 0.2465929729441158 chrMT 16571 6293 0.3797598213746907 0.9231260449003393 chrX 155270560 7589687 0.048880399478175386 0.3673060544517624 chrY 59373566 310335 0.0052268209728214745 0.12389582219034974