BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063604.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,525,199 number of mapped reads = 3,352,769 (95.11%) number of supplementary alignments = 23,855 (0.68%) number of secondary alignments = 0 number of mapped bases = 215,163,467 bp number of sequenced bases = 215,081,455 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 342,212 duplication rate = 8.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4378 >>>>>>> ACTG content number of A's = 55,577,725 bp (25.84%) number of C's = 38,958,206 bp (18.11%) number of T's = 69,790,466 bp (32.45%) number of G's = 50,729,971 bp (23.59%) number of N's = 25,087 bp (0.01%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,114,546 number of insertions = 12,698 mapped reads with insertion percentage = 0.38% number of deletions = 47,470 mapped reads with deletion percentage = 1.4% homopolymer indels = 44.43% >>>>>>> Coverage mean coverageData = 0.0695X std coverageData = 0.7133X There is a 5.36% of reference with a coverageData >= 1X There is a 1.09% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.07% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 20282843 0.08137529575101841 1.374716922526684 chr2 243199373 22251365 0.09149433539041238 1.146777658067308 chr3 198022430 13027641 0.06578871393508301 0.32011389885168895 chr4 191154276 12000899 0.06278122180222638 0.3211237897311902 chr5 180915260 8639366 0.047753661023398467 0.2781090549221764 chr6 171115067 17203358 0.10053678090194126 0.5415893212652881 chr7 159138663 17140915 0.10771056308296369 1.3870714230730423 chr8 146364022 9017043 0.06160696376599982 0.49645645317986753 chr9 141213431 6119661 0.04333625319251679 0.5228851489541649 chr10 135534747 9669055 0.07134004536858729 0.42161234649016666 chr11 135006516 9283959 0.06876674752498613 0.42467889454953545 chr12 133851895 11590718 0.0865936040726207 0.4184585636087965 chr13 115169878 5911361 0.051327318415671154 0.3237664182378034 chr14 107349540 4706389 0.043841724892347 0.35554805923039706 chr15 102531392 3883606 0.037877238611956035 0.28242999365620847 chr16 90354753 3996660 0.044232980195297526 0.2962479845088783 chr17 81195210 6262918 0.07713408217061081 0.37242706200567227 chr18 78077248 5667134 0.07258368020348258 0.9799659044266517 chr19 59128983 5049265 0.08539407823063691 0.8746806047722091 chr20 63025520 3419291 0.05425248375578654 0.3185467240013772 chr21 48129895 3963424 0.08234848632019663 0.36643446598092266 chr22 51304566 1608705 0.031355981064141544 0.21288186982205168 chrMT 16571 270119 16.300706052742743 8.645180012627227 chrX 155270560 13693897 0.08819377607706187 0.4370336958551191 chrY 59373566 503875 0.008486520752349623 0.1991756666545958