BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708619.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 = 3,400,589 number of mapped reads = 2,447,260 (71.97%) number of supplementary alignments = 863 (0.03%) number of secondary alignments = 0 number of mapped bases = 119,058,103 bp number of sequenced bases = 119,034,687 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,724 duplication rate = 2.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6053 >>>>>>> ACTG content number of A's = 34,894,791 bp (29.31%) number of C's = 22,565,261 bp (18.96%) number of T's = 37,436,851 bp (31.45%) number of G's = 24,127,357 bp (20.27%) number of N's = 10,427 bp (0.01%) GC percentage = 39.23% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 757,567 number of insertions = 5,711 mapped reads with insertion percentage = 0.23% number of deletions = 15,244 mapped reads with deletion percentage = 0.62% homopolymer indels = 48.12% >>>>>>> Coverage mean coverageData = 0.0385X std coverageData = 0.3816X There is a 3.31% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9275986 0.03721549805085541 0.6969187503182278 chr2 243199373 10248741 0.042141313415310494 0.41234306688613065 chr3 198022430 8029042 0.04054612399211544 0.23017966848080143 chr4 191154276 7997931 0.04184018881168005 0.23663065992567148 chr5 180915260 7550211 0.04173341154306165 0.2349456165994137 chr6 171115067 7143550 0.04174705433741846 0.32393536073438545 chr7 159138663 6846238 0.043020582622338606 0.569609194947499 chr8 146364022 6355114 0.04341991913832485 0.6133462861795939 chr9 141213431 5054061 0.03579022876372149 0.3043450918749142 chr10 135534747 5300853 0.039110656988941735 0.3009203471661115 chr11 135006516 5431519 0.04023153223211834 0.30596767584163903 chr12 133851895 5299834 0.03959476255453836 0.23474500086212868 chr13 115169878 4012647 0.034841115313155056 0.21617517497654445 chr14 107349540 3678142 0.034263230191764214 0.22995087589008695 chr15 102531392 3388888 0.03305219927180936 0.20725529432310963 chr16 90354753 3054793 0.033808879982218536 0.22331494839342228 chr17 81195210 2889821 0.035591028091435446 0.2513321838804057 chr18 78077248 3274064 0.041933650120455065 0.5918113553075379 chr19 59128983 2093367 0.035403399378609306 0.5195401352685736 chr20 63025520 2342853 0.03717308480755097 0.22727847531917159 chr21 48129895 1556349 0.03233643040359843 0.22287996603415566 chr22 51304566 1166609 0.022738892284947892 0.1699754577131733 chrMT 16571 5184 0.31283567678474444 0.6477977120527979 chrX 155270560 6774650 0.043631258881271506 0.26622086117677524 chrY 59373566 287656 0.004844849642347573 0.08676004742499421