BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708588.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 = 3,941,668 number of mapped reads = 3,793,835 (96.25%) number of supplementary alignments = 88 (0%) number of secondary alignments = 0 number of mapped bases = 189,239,181 bp number of sequenced bases = 189,222,701 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,863 duplication rate = 0.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7356 >>>>>>> ACTG content number of A's = 58,637,368 bp (30.99%) number of C's = 35,857,977 bp (18.95%) number of T's = 58,355,160 bp (30.84%) number of G's = 36,365,582 bp (19.22%) number of N's = 6,614 bp (0%) GC percentage = 38.17% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 271,668 number of insertions = 11,895 mapped reads with insertion percentage = 0.31% number of deletions = 9,650 mapped reads with deletion percentage = 0.25% homopolymer indels = 49.58% >>>>>>> Coverage mean coverageData = 0.0611X std coverageData = 0.2561X There is a 5.75% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 14518507 0.05824862919799907 0.25306938561838394 chr2 243199373 17279266 0.07104979666209912 0.2809472479773922 chr3 198022430 14572358 0.07358943125786306 0.27937690286492156 chr4 191154276 14791600 0.07738042961696551 0.2856857168415981 chr5 180915260 13381854 0.07396752490641198 0.2796670261538267 chr6 171115067 12283227 0.0717834333080675 0.27555084527049006 chr7 159138663 10685867 0.06714815116927306 0.26744234418134005 chr8 146364022 10319181 0.07050353535652361 0.2733914429502476 chr9 141213431 7866945 0.05570960881192668 0.24418165114051732 chr10 135534747 7984712 0.05891265654555728 0.24966267316621005 chr11 135006516 8908953 0.06598905937251207 0.26581034531692116 chr12 133851895 8642381 0.06456674371326607 0.2618150914494084 chr13 115169878 7139197 0.06198840464170675 0.2570132307352959 chr14 107349540 5671579 0.05283282070887309 0.23730994043987066 chr15 102531392 4917871 0.04796453948464876 0.22680298050932868 chr16 90354753 3356024 0.037142749977967404 0.19833974211359023 chr17 81195210 2999802 0.03694555380791552 0.19845043367856863 chr18 78077248 5418954 0.06940503333314207 0.2711723596984535 chr19 59128983 1512449 0.025578809633847413 0.16373331172479574 chr20 63025520 3104661 0.049260378970296476 0.22927620163917017 chr21 48129895 2291419 0.04760905877729424 0.22646488506143223 chr22 51304566 1057839 0.020618808080356824 0.14786193377392737 chrMT 16571 332 0.020035000905195825 0.14684918817794604 chrX 155270560 10291503 0.06628109668697015 0.2648204395575498 chrY 59373566 242700 0.004087677671238409 0.06642607794667926