BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818849.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 = 1,034,999 number of mapped reads = 1,022,595 (98.8%) number of supplementary alignments = 15,950 (1.54%) number of secondary alignments = 0 number of mapped bases = 94,728,543 bp number of sequenced bases = 94,669,792 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 195,780 duplication rate = 16.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.501 >>>>>>> ACTG content number of A's = 27,126,373 bp (28.65%) number of C's = 19,558,106 bp (20.66%) number of T's = 26,668,965 bp (28.17%) number of G's = 21,314,949 bp (22.52%) number of N's = 1,399 bp (0%) GC percentage = 43.17% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 564,149 number of insertions = 15,278 mapped reads with insertion percentage = 1.45% number of deletions = 30,879 mapped reads with deletion percentage = 2.95% homopolymer indels = 38.93% >>>>>>> Coverage mean coverageData = 0.0306X std coverageData = 0.3758X There is a 2.28% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 7318252 0.029361018121595774 0.5006762718374358 chr2 243199373 7461414 0.030680235347481755 0.5076676535308399 chr3 198022430 6171223 0.03116426255348952 0.2242101060512118 chr4 191154276 5064097 0.02649219837488752 0.26936241334765726 chr5 180915260 4105376 0.02269225934838222 0.19608249409139797 chr6 171115067 4991285 0.029169173045410432 0.22882797117634557 chr7 159138663 8917397 0.05603538971544583 0.8650431450064419 chr8 146364022 7716580 0.052721836244702266 0.3420983956432959 chr9 141213431 3622434 0.025652191681398918 0.31439565575316775 chr10 135534747 4504820 0.03323738081718631 0.43199246583425527 chr11 135006516 4379142 0.03243652328603162 0.25691871218538725 chr12 133851895 3827042 0.028591616129155287 0.21581236294035974 chr13 115169878 3092286 0.026849780981794562 0.20779425199460078 chr14 107349540 2484529 0.023144291070087492 0.20606296304166571 chr15 102531392 2678104 0.026119844349718768 0.20523549492433532 chr16 90354753 2390810 0.026460257159908344 0.3770107571152762 chr17 81195210 2234979 0.02752599568373553 0.2533484902275673 chr18 78077248 1881901 0.024103065210495125 0.3428360799261581 chr19 59128983 1614753 0.027308993290143347 0.4297331735003263 chr20 63025520 4068227 0.06454888432495282 0.3422643277289276 chr21 48129895 943887 0.019611241620202995 0.20313665647957158 chr22 51304566 893473 0.017415077636559678 0.18056001199864094 chrMT 16571 57123 3.4471667370707864 2.8811531612815897 chrX 155270560 3965923 0.025542015176605277 0.22635940094247683 chrY 59373566 343486 0.005785167089340734 0.41207490374957073