BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231741.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 = 1,811,884 number of mapped reads = 1,026,238 (56.64%) number of supplementary alignments = 7,798 (0.43%) number of secondary alignments = 0 number of mapped bases = 64,955,956 bp number of sequenced bases = 64,919,448 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 164,818 duplication rate = 12.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6965 >>>>>>> ACTG content number of A's = 17,146,493 bp (26.41%) number of C's = 12,408,872 bp (19.11%) number of T's = 20,249,187 bp (31.19%) number of G's = 15,103,416 bp (23.26%) number of N's = 11,480 bp (0.02%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 589,142 number of insertions = 5,577 mapped reads with insertion percentage = 0.54% number of deletions = 21,013 mapped reads with deletion percentage = 2.02% homopolymer indels = 46.79% >>>>>>> Coverage mean coverageData = 0.021X std coverageData = 0.2658X There is a 1.06% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 5549824 0.02226603880758235 0.2878697854652543 chr2 243199373 4525265 0.018607223136220832 0.28935046275759957 chr3 198022430 6824397 0.03446274747764685 0.31926638745150965 chr4 191154276 3105413 0.016245584796648754 0.22082167646108353 chr5 180915260 5057553 0.027955369823418987 0.2881352499584219 chr6 171115067 3209662 0.01875733128748972 0.24636830280604372 chr7 159138663 3615580 0.022719683148274283 0.29188243571649153 chr8 146364022 2911653 0.019893228952125953 0.2693905646495902 chr9 141213431 2284053 0.016174474225472222 0.23085693853671854 chr10 135534747 3258814 0.024044122058235 0.2752142392598649 chr11 135006516 2386077 0.017673791389446712 0.2486488613680301 chr12 133851895 2413704 0.018032647203089655 0.2301658527115945 chr13 115169878 1631107 0.01416261811096127 0.22683814465958888 chr14 107349540 1752716 0.016327186870106754 0.22413602431573582 chr15 102531392 1648732 0.01608026544689845 0.21836453898819835 chr16 90354753 1537375 0.017014876904151353 0.23253135574891234 chr17 81195210 3402033 0.04189942978163367 0.3558887318419357 chr18 78077248 2554036 0.03271165500095495 0.3837417391192913 chr19 59128983 1218726 0.02061131340615143 0.2678318747717426 chr20 63025520 1216582 0.019303006147351105 0.24619594449734244 chr21 48129895 1840271 0.038235508305181215 0.33667954287883595 chr22 51304566 720179 0.014037327593805198 0.20220759742960587 chrMT 16571 32486 1.9604127692957576 2.9934545529830157 chrX 155270560 1975787 0.012724801147107346 0.19347187059600712 chrY 59373566 283931 0.004782111285011919 0.10884146899298819