BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617392.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 29,600,971 (92.5%) number of supplementary alignments = 441,369 (1.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,880,059 number of mapped paired reads (second in pair) = 14,720,912 number of mapped paired reads (both in pair) = 29,002,640 number of mapped paired reads (singletons) = 598,331 number of mapped bases = 2,908,458,336 bp number of sequenced bases = 2,907,832,545 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,331,103 duplication rate = 4.1% >>>>>>> Insert size mean insert size = 48,265.4193 std insert size = 2,091,744.3428 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 53.8707 >>>>>>> ACTG content number of A's = 869,247,483 bp (29.89%) number of C's = 582,980,698 bp (20.05%) number of T's = 858,474,924 bp (29.52%) number of G's = 594,580,955 bp (20.45%) number of N's = 2,548,485 bp (0.09%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.012 number of mismatches = 34,344,378 number of insertions = 382,699 mapped reads with insertion percentage = 1.28% number of deletions = 281,204 mapped reads with deletion percentage = 0.93% homopolymer indels = 38.88% >>>>>>> Coverage mean coverageData = 0.9395X std coverageData = 2.872X There is a 29.4% of reference with a coverageData >= 1X There is a 16.82% of reference with a coverageData >= 2X There is a 10.74% of reference with a coverageData >= 3X There is a 7.4% of reference with a coverageData >= 4X There is a 5.37% of reference with a coverageData >= 5X There is a 4.04% of reference with a coverageData >= 6X There is a 3.12% of reference with a coverageData >= 7X There is a 2.46% of reference with a coverageData >= 8X There is a 1.98% of reference with a coverageData >= 9X There is a 1.62% of reference with a coverageData >= 10X There is a 1.34% of reference with a coverageData >= 11X There is a 1.12% of reference with a coverageData >= 12X There is a 0.95% of reference with a coverageData >= 13X There is a 0.81% of reference with a coverageData >= 14X There is a 0.69% of reference with a coverageData >= 15X There is a 0.6% of reference with a coverageData >= 16X There is a 0.52% of reference with a coverageData >= 17X There is a 0.46% of reference with a coverageData >= 18X There is a 0.4% of reference with a coverageData >= 19X There is a 0.35% of reference with a coverageData >= 20X There is a 0.31% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.16% of reference with a coverageData >= 27X There is a 0.15% of reference with a coverageData >= 28X There is a 0.13% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.07% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 186914231 0.7499047755632272 2.700521225234995 chr2 243199373 290402408 1.1940919272024604 3.0175028266347037 chr3 198022430 245782861 1.2411869756370528 3.353782843047042 chr4 191154276 140201492 0.7334467997985041 2.237304035855366 chr5 180915260 186649412 1.0316952367644388 2.8261475507216924 chr6 171115067 133641112 0.7810014298740858 2.5542353212455966 chr7 159138663 217654063 1.3677007139364996 3.1756272181587906 chr8 146364022 128751848 0.8796686934443493 3.1820297756859985 chr9 141213431 116675174 0.8262328389995708 2.5828450017804565 chr10 135534747 93190451 0.6875760870384036 2.3717632685969336 chr11 135006516 215968959 1.5996928548248739 3.7775029752182636 chr12 133851895 138402751 1.0339991899255516 2.7203569403698737 chr13 115169878 126799129 1.1009747618209684 2.7324194003134075 chr14 107349540 84265672 0.7849653757249448 2.837270181041453 chr15 102531392 66507275 0.6486528047917266 2.306118303869423 chr16 90354753 72940651 0.8072696629473383 3.251847928017162 chr17 81195210 89126176 1.097677757099218 3.656651490446375 chr18 78077248 41744289 0.5346536932244333 1.9723433265997017 chr19 59128983 41239188 0.6974445679202702 2.2796848864926154 chr20 63025520 98481706 1.562568718195423 4.619905486781163 chr21 48129895 39846653 0.8278981909268657 2.466495765413312 chr22 51304566 23023542 0.44876204585767276 2.005530270015281 chrMT 16571 178292 10.759278257196307 4.834722328294665 chrX 155270560 127785911 0.822988665720018 2.5177187694159704 chrY 59373566 2285090 0.038486655829296154 0.5519715051136898