BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080643.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 = 1,528,159 number of mapped reads = 1,396,153 (91.36%) number of supplementary alignments = 14,859 (0.97%) number of secondary alignments = 0 number of mapped bases = 93,185,228 bp number of sequenced bases = 93,150,145 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,246 duplication rate = 3.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.75 >>>>>>> ACTG content number of A's = 25,352,387 bp (27.22%) number of C's = 17,370,236 bp (18.65%) number of T's = 29,331,319 bp (31.49%) number of G's = 21,092,160 bp (22.64%) number of N's = 4,043 bp (0%) GC percentage = 41.29% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 641,712 number of insertions = 6,957 mapped reads with insertion percentage = 0.49% number of deletions = 21,625 mapped reads with deletion percentage = 1.53% homopolymer indels = 47.44% >>>>>>> Coverage mean coverageData = 0.0301X std coverageData = 0.2518X There is a 2.63% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 11142192 0.04470276525409339 0.3519934531895588 chr2 243199373 6143399 0.025260751803007322 0.34076530087739565 chr3 198022430 5668309 0.028624580558879113 0.18765192754128582 chr4 191154276 4078428 0.021335792666233633 0.16849285297691086 chr5 180915260 4217861 0.0233140145281277 0.16896927325273245 chr6 171115067 5646784 0.03299992279464204 0.24628738988935545 chr7 159138663 5755547 0.0361668678842677 0.445069445532293 chr8 146364022 11034281 0.07538929888111438 0.35252752499476764 chr9 141213431 2905462 0.020574969246374305 0.19383283300597423 chr10 135534747 5134514 0.03788337761090888 0.2324578356792102 chr11 135006516 3857885 0.028575546679539526 0.22322531394882197 chr12 133851895 2859573 0.021363709493989608 0.163119139006374 chr13 115169878 1695626 0.014722825355428439 0.13477318766801077 chr14 107349540 1814713 0.01690471146872171 0.14618263777754026 chr15 102531392 1583902 0.015447971290587765 0.14561745168103385 chr16 90354753 2361527 0.026136167955658072 0.1844337105140055 chr17 81195210 1531940 0.018867369146529703 0.16125193444683986 chr18 78077248 2927888 0.03749988729110944 0.27948436775040314 chr19 59128983 1536273 0.025981725408671413 0.23234982084451808 chr20 63025520 2831241 0.044922136302881756 0.23848608822300604 chr21 48129895 1363442 0.028328380936629927 0.1898025703748322 chr22 51304566 927136 0.018071218066633678 0.1484047410187551 chrMT 16571 15795 0.9531712027035182 1.0375100500056356 chrX 155270560 5970182 0.03845018656466493 0.22986640144578807 chrY 59373566 181328 0.003054019022539424 0.06558398314982798