BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080784.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,580,615 number of mapped reads = 2,298,946 (89.09%) number of supplementary alignments = 25,546 (0.99%) number of secondary alignments = 0 number of mapped bases = 153,133,244 bp number of sequenced bases = 153,080,063 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,545 duplication rate = 3.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3252 >>>>>>> ACTG content number of A's = 43,730,512 bp (28.57%) number of C's = 29,653,595 bp (19.37%) number of T's = 46,606,740 bp (30.45%) number of G's = 33,086,022 bp (21.61%) number of N's = 3,194 bp (0%) GC percentage = 40.98% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,129,828 number of insertions = 11,440 mapped reads with insertion percentage = 0.49% number of deletions = 33,261 mapped reads with deletion percentage = 1.43% homopolymer indels = 47.42% >>>>>>> Coverage mean coverageData = 0.0495X std coverageData = 0.334X There is a 3.92% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 19797651 0.07942869277745952 0.5374083494289299 chr2 243199373 11166883 0.04591657808262524 0.3925207352703721 chr3 198022430 10005836 0.05052880120701478 0.2720547393908671 chr4 191154276 8554218 0.044750335587575345 0.2624357415564838 chr5 180915260 11142529 0.06158976860216214 0.3027247981416863 chr6 171115067 10396196 0.060755585012277145 0.3658927148869888 chr7 159138663 9837093 0.06181460127008859 0.3831942671507197 chr8 146364022 7232755 0.04941620830835053 0.3933381584198002 chr9 141213431 5468343 0.038723958204797106 0.28158897903857616 chr10 135534747 6150758 0.0453814105692026 0.31172836696626177 chr11 135006516 6481033 0.04800533479435911 0.29059902509241253 chr12 133851895 6335917 0.047335280535251295 0.2660025781949632 chr13 115169878 6319197 0.05486848740084625 0.28917367000144567 chr14 107349540 3807464 0.035467911646384326 0.23720310705510472 chr15 102531392 3699815 0.03608470467269185 0.24101823430627556 chr16 90354753 3058452 0.033849375914956015 0.2338141589063041 chr17 81195210 3745299 0.0461270929652131 0.2739667894406721 chr18 78077248 2203809 0.02822600765846665 0.4090621294295109 chr19 59128983 2537229 0.042910073389897475 0.3513370664260432 chr20 63025520 2368923 0.03758672677353555 0.23763090394329556 chr21 48129895 2571545 0.053429266778994636 0.28713861618336156 chr22 51304566 1282186 0.02499165473887841 0.19094956148291453 chrMT 16571 11309 0.6824573049302999 0.9792925763731586 chrX 155270560 8633606 0.05560362505293985 0.29623562243657003 chrY 59373566 325198 0.00547715122921874 0.10760185972726792