BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695985.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 10,991,054 number of mapped reads = 9,876,862 (89.86%) number of supplementary alignments = 14,407 (0.13%) number of secondary alignments = 0 number of mapped bases = 1,323,603,727 bp number of sequenced bases = 1,313,963,642 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,895,784 duplication rate = 16.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.0514 >>>>>>> ACTG content number of A's = 373,978,072 bp (28.46%) number of C's = 280,572,769 bp (21.35%) number of T's = 370,059,888 bp (28.16%) number of G's = 289,352,913 bp (22.02%) number of N's = 0 bp (0%) GC percentage = 43.37% >>>>>>> Mismatches and indels general error rate = 0.0209 number of mismatches = 18,879,815 number of insertions = 7,831,840 mapped reads with insertion percentage = 47.97% number of deletions = 8,652,982 mapped reads with deletion percentage = 51.58% homopolymer indels = 37.21% >>>>>>> Coverage mean coverageData = 0.4276X std coverageData = 1.4174X There is a 17.49% of reference with a coverageData >= 1X There is a 9.29% of reference with a coverageData >= 2X There is a 5.33% of reference with a coverageData >= 3X There is a 3.25% of reference with a coverageData >= 4X There is a 2.08% of reference with a coverageData >= 5X There is a 1.38% of reference with a coverageData >= 6X There is a 0.94% of reference with a coverageData >= 7X There is a 0.66% of reference with a coverageData >= 8X There is a 0.47% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.25% of reference with a coverageData >= 11X There is a 0.19% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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 117944267 0.4731954790194886 1.5963475060483392 chr2 243199373 113965987 0.4686113520531157 1.6376319027873183 chr3 198022430 88891361 0.44889541553449275 1.3438704038533904 chr4 191154276 69067089 0.3613159508919382 1.2862867291774212 chr5 180915260 79162253 0.4375653717657648 1.3282472263765135 chr6 171115067 75108040 0.4389329432924805 1.333770794202437 chr7 159138663 67641272 0.42504612471200665 1.3162220435853327 chr8 146364022 70022870 0.47841586370180506 1.4456536823426782 chr9 141213431 56699762 0.40151819553198165 1.4419716105918932 chr10 135534747 66446763 0.4902562956789228 1.4789928164227397 chr11 135006516 67568296 0.500481739710993 1.4979560692116336 chr12 133851895 61000464 0.4557310451226708 1.3706360615893585 chr13 115169878 36837799 0.31985619538469945 1.1396361344764043 chr14 107349540 49853780 0.46440608874523354 1.5039602837174417 chr15 102531392 43392192 0.42320884515056617 1.3436875426566486 chr16 90354753 45517891 0.503768639597742 1.6991478305490662 chr17 81195210 38626110 0.4757190725906122 1.4612436229198433 chr18 78077248 34654888 0.44385386124265036 1.5915729905535272 chr19 59128983 23169243 0.39184240662485265 1.3571985900559844 chr20 63025520 37772299 0.5993175304225971 1.658534325722485 chr21 48129895 16422290 0.34120768391454004 1.754967019194465 chr22 51304566 19093566 0.3721611444876076 1.288405062504082 chrMT 16571 141195 8.520608291593748 9.441105862886237 chrX 155270560 37527643 0.24169194082896334 0.886308978341347 chrY 59373566 7076407 0.11918447007208562 0.8176051500343161