BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708601.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,156,460 number of mapped reads = 4,044,025 (97.29%) number of supplementary alignments = 95 (0%) number of secondary alignments = 0 number of mapped bases = 201,727,567 bp number of sequenced bases = 201,710,024 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,799 duplication rate = 0.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.735 >>>>>>> ACTG content number of A's = 62,503,676 bp (30.99%) number of C's = 38,243,127 bp (18.96%) number of T's = 62,213,759 bp (30.84%) number of G's = 38,742,196 bp (19.21%) number of N's = 7,266 bp (0%) GC percentage = 38.17% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 295,147 number of insertions = 12,931 mapped reads with insertion percentage = 0.32% number of deletions = 10,313 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.27% >>>>>>> Coverage mean coverageData = 0.0652X std coverageData = 0.2648X There is a 6.09% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 15538928 0.06234258489570624 0.2602690060126478 chr2 243199373 17639263 0.07253005130074903 0.27835060917279614 chr3 198022430 15386592 0.0777012583877493 0.28772776082766716 chr4 191154276 15843442 0.08288301120713616 0.2971610665658899 chr5 180915260 13907964 0.07687557146920608 0.2858503732265678 chr6 171115067 13875396 0.08108810196123759 0.2944849778668891 chr7 159138663 11126975 0.06991999800827785 0.27367041799774355 chr8 146364022 10763049 0.07353616587551823 0.28026366259508106 chr9 141213431 8697220 0.06158918410529945 0.257927955738961 chr10 135534747 8334442 0.0614930280572258 0.25594121362582073 chr11 135006516 9412671 0.06972012373091681 0.2746525168502729 chr12 133851895 8881258 0.06635138038202597 0.26690111795835025 chr13 115169878 8111249 0.07042856292684446 0.27561745899571116 chr14 107349540 6540307 0.06092533791947315 0.2567905001678237 chr15 102531392 5337746 0.05205962677264735 0.2372969522360037 chr16 90354753 3643243 0.04032154235427991 0.20783111660750647 chr17 81195210 3260412 0.04015522590556758 0.20738106916832774 chr18 78077248 5646790 0.07232311774103513 0.277820482348355 chr19 59128983 1610851 0.027243001964028367 0.16996822115654242 chr20 63025520 3205342 0.05085784298170011 0.23357598925039957 chr21 48129895 2407985 0.050030963084378224 0.23399474264425696 chr22 51304566 1106363 0.02156461083795154 0.15184768746932614 chrMT 16571 150 0.009051958240299317 0.09471019106894038 chrX 155270560 11193591 0.07209087801319194 0.2775117290845025 chrY 59373566 256338 0.004317375850391065 0.06884729780269241