BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082678.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 = 3,090,034 number of mapped reads = 2,857,810 (92.48%) number of supplementary alignments = 11,018 (0.36%) number of secondary alignments = 0 number of mapped bases = 188,824,031 bp number of sequenced bases = 188,752,233 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,411 duplication rate = 3.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7622 >>>>>>> ACTG content number of A's = 51,548,697 bp (27.31%) number of C's = 32,343,638 bp (17.14%) number of T's = 62,983,817 bp (33.37%) number of G's = 41,826,471 bp (22.16%) number of N's = 49,610 bp (0.03%) GC percentage = 39.29% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,697,167 number of insertions = 16,849 mapped reads with insertion percentage = 0.58% number of deletions = 44,695 mapped reads with deletion percentage = 1.55% homopolymer indels = 48.97% >>>>>>> Coverage mean coverageData = 0.061X std coverageData = 0.4771X There is a 5.07% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 18986677 0.07617504391292972 0.7247202781272418 chr2 243199373 17055879 0.0701312622216341 0.6608494832736279 chr3 198022430 16253673 0.08207995932581981 0.33443423008211265 chr4 191154276 9849668 0.051527322360290805 0.27166222491962183 chr5 180915260 12219606 0.06754325754499647 0.30572295401386257 chr6 171115067 12413516 0.07254484492590006 0.5835036593999592 chr7 159138663 8157417 0.05125980604725829 0.5327157698075774 chr8 146364022 16997887 0.11613432568831704 0.5817395871236051 chr9 141213431 5818037 0.041200309055588344 0.5213525885343345 chr10 135534747 7983691 0.05890512342196647 0.3873158640304255 chr11 135006516 7863475 0.058245151663642664 0.40324523685332775 chr12 133851895 5928861 0.04429418799039042 0.25167503267956287 chr13 115169878 4718596 0.040970747576896796 0.23027831927771406 chr14 107349540 4030332 0.03754400810660204 0.2778495809155229 chr15 102531392 3741115 0.036487508137995436 0.21782101470232307 chr16 90354753 6369357 0.07049277197404324 0.3452187094062752 chr17 81195210 4374240 0.05387312872274116 0.33897416171925787 chr18 78077248 5120889 0.06558746793944377 1.020647242990292 chr19 59128983 2551495 0.04315134254888166 0.5432360705282846 chr20 63025520 4386044 0.06959155592845565 0.3175845896045654 chr21 48129895 3067581 0.06373546005034916 0.3059861706535347 chr22 51304566 2476044 0.048261669341477326 0.2522572220257342 chrMT 16571 4773 0.2880333112063243 0.6330537558855276 chrX 155270560 8110750 0.05223623847302412 0.3403596060317443 chrY 59373566 344428 0.00580103273567904 0.12426316482613879