BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472489.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,585,898 number of mapped reads = 15,413,989 (98.9%) number of supplementary alignments = 68,262 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,729,426 number of mapped paired reads (second in pair) = 7,684,563 number of mapped paired reads (both in pair) = 15,322,550 number of mapped paired reads (singletons) = 91,439 number of mapped bases = 1,518,420,737 bp number of sequenced bases = 1,518,223,699 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,821,180 duplication rate = 45.94% >>>>>>> Insert size mean insert size = 31,142.0964 std insert size = 1,712,690.2151 median insert size = 245 >>>>>>> Mapping quality mean mapping quality = 55.0073 >>>>>>> ACTG content number of A's = 432,192,097 bp (28.47%) number of C's = 328,788,615 bp (21.66%) number of T's = 429,566,595 bp (28.29%) number of G's = 327,438,464 bp (21.57%) number of N's = 237,928 bp (0.02%) GC percentage = 43.22% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 9,193,898 number of insertions = 86,624 mapped reads with insertion percentage = 0.56% number of deletions = 80,305 mapped reads with deletion percentage = 0.51% homopolymer indels = 44.37% >>>>>>> Coverage mean coverageData = 0.4905X std coverageData = 18.263X There is a 5.09% of reference with a coverageData >= 1X There is a 2.29% of reference with a coverageData >= 2X There is a 1.01% of reference with a coverageData >= 3X There is a 0.68% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 137698266 0.5524490388330868 20.246125246019457 chr2 243199373 97962700 0.402808193095136 14.889741013664228 chr3 198022430 162551203 0.820872680938215 18.86999449922266 chr4 191154276 53477284 0.2797598103429295 12.226014355788799 chr5 180915260 74560912 0.4121316908258596 16.42066321428467 chr6 171115067 112607638 0.6580813716421594 22.384161344000187 chr7 159138663 74672844 0.46923131432868703 17.92884939526538 chr8 146364022 114358486 0.7813292121748335 28.206362736197203 chr9 141213431 117216910 0.8300691313137204 23.688396335544898 chr10 135534747 33758438 0.24907589195558832 9.571872924641694 chr11 135006516 68301480 0.5059124701803281 17.795231343662817 chr12 133851895 118272169 0.8836047408966455 31.430809021852948 chr13 115169878 48918695 0.42475251211084897 25.047844250009405 chr14 107349540 33209892 0.3093622199033177 12.469671241681365 chr15 102531392 31358890 0.3058467205829021 11.94275637382348 chr16 90354753 53337806 0.5903154425091506 15.17747357755457 chr17 81195210 38112910 0.469398502694925 13.364583828141956 chr18 78077248 26516097 0.33961362213996066 18.02208586389777 chr19 59128983 20346887 0.3441102141059994 9.223828263558493 chr20 63025520 19481188 0.3090999963189514 11.780448718710437 chr21 48129895 6425548 0.13350430122484164 4.393050445330494 chr22 51304566 7624218 0.14860700702545657 5.073482023377104 chrMT 16571 2808 0.16945265825840322 0.5200799838920813 chrX 155270560 62646536 0.40346692895291936 13.16337312883037 chrY 59373566 5000932 0.08422825740330302 4.657237728778357