BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004022.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 = 2,956,597 number of mapped reads = 2,651,105 (89.67%) number of supplementary alignments = 19,646 (0.66%) number of secondary alignments = 0 number of mapped bases = 172,206,044 bp number of sequenced bases = 172,122,599 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,533 duplication rate = 3.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1064 >>>>>>> ACTG content number of A's = 45,736,486 bp (26.57%) number of C's = 32,451,882 bp (18.85%) number of T's = 53,078,830 bp (30.84%) number of G's = 40,822,482 bp (23.72%) number of N's = 32,919 bp (0.02%) GC percentage = 42.57% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,456,494 number of insertions = 13,054 mapped reads with insertion percentage = 0.49% number of deletions = 51,252 mapped reads with deletion percentage = 1.91% homopolymer indels = 45.74% >>>>>>> Coverage mean coverageData = 0.0556X std coverageData = 0.453X There is a 4.63% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.13% 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 13973462 0.05606189442553084 0.87869357768458 chr2 243199373 15728274 0.06467234600970785 0.6135048327934357 chr3 198022430 11842117 0.059801897189121454 0.2839173710222824 chr4 191154276 13427122 0.07024233138263672 0.30885462060915747 chr5 180915260 10057752 0.055593718296621304 0.2711862016162423 chr6 171115067 14100410 0.082403088443404 0.4196882782846505 chr7 159138663 11575544 0.0727387284886263 0.6860750186732111 chr8 146364022 9643733 0.06588868540384876 0.4569420664424392 chr9 141213431 5662119 0.04009617895340281 0.32575740498096223 chr10 135534747 6823526 0.05034521516463966 0.40638956970626333 chr11 135006516 6669119 0.049398497180684224 0.30257378908736793 chr12 133851895 4695396 0.035079040158527454 0.22353915668675592 chr13 115169878 5425650 0.04710997436326189 0.2503174976049952 chr14 107349540 2213538 0.020619911366178186 0.21828706704381845 chr15 102531392 4449752 0.04339892313175656 0.26083144726309815 chr16 90354753 4084394 0.045203975047112356 0.2684284324743564 chr17 81195210 5147609 0.06339793936120124 0.3100835513016875 chr18 78077248 3926345 0.05028795328441904 0.5288378749133714 chr19 59128983 3311488 0.05600448091589872 0.6470496450871069 chr20 63025520 4832846 0.07668077946838042 0.34319275869280447 chr21 48129895 2074537 0.043102878159198145 0.25142050347316236 chr22 51304566 1227324 0.023922315218493417 0.17855574610107183 chrMT 16571 75321 4.5453503107839 4.097893796659468 chrX 155270560 10857621 0.06992710659380633 0.3361106653858114 chrY 59373566 381045 0.006417754998916521 0.10383721707541949