BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068124.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 = 4,910,782 number of mapped reads = 4,686,598 (95.43%) number of supplementary alignments = 35,988 (0.73%) number of secondary alignments = 0 number of mapped bases = 308,015,284 bp number of sequenced bases = 307,879,616 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 466,025 duplication rate = 7.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0791 >>>>>>> ACTG content number of A's = 83,268,078 bp (27.05%) number of C's = 56,278,182 bp (18.28%) number of T's = 98,926,008 bp (32.13%) number of G's = 69,370,643 bp (22.53%) number of N's = 36,705 bp (0.01%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,701,222 number of insertions = 20,403 mapped reads with insertion percentage = 0.43% number of deletions = 76,033 mapped reads with deletion percentage = 1.6% homopolymer indels = 45.68% >>>>>>> Coverage mean coverageData = 0.0995X std coverageData = 1.0091X There is a 7.33% of reference with a coverageData >= 1X There is a 1.73% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 28200719 0.11314202101827461 2.1338826660780486 chr2 243199373 29104010 0.119671402277834 1.0322127710585296 chr3 198022430 14503285 0.07324061723714834 0.34778545334495375 chr4 191154276 14940551 0.07815964838788121 0.39860575537610143 chr5 180915260 15232395 0.08419629720566413 0.37665297094309835 chr6 171115067 19190298 0.11214849946556722 0.6063809711647644 chr7 159138663 24921040 0.15659953106430208 2.0389002872001494 chr8 146364022 13923963 0.09513241580639265 1.3138968645427438 chr9 141213431 10649774 0.07541615499732458 0.729569039468526 chr10 135534747 17405663 0.12842214550339626 0.7792957533659363 chr11 135006516 16837055 0.1247129064496413 0.5603023281574008 chr12 133851895 20121218 0.1503244911101184 0.5554755283068507 chr13 115169878 8094236 0.07028084200974842 0.35531828682978933 chr14 107349540 7822609 0.07287044732562431 0.43432543506887106 chr15 102531392 8293228 0.08088476941774086 0.3895444290194876 chr16 90354753 9123787 0.10097738853870808 0.47405404455405914 chr17 81195210 7432772 0.09154200106139267 0.40806866838583616 chr18 78077248 8071870 0.10338312641347196 1.3928038147579724 chr19 59128983 5774461 0.09765872347237901 1.4840038734291428 chr20 63025520 3365995 0.05340685804734336 0.3440912563845371 chr21 48129895 6487132 0.134783838610078 0.5067775020850945 chr22 51304566 2582446 0.050335597810144225 0.2779069252171687 chrMT 16571 430255 25.96433528453322 14.314337736378006 chrX 155270560 14577464 0.09388427529339753 0.4861005610586686 chrY 59373566 929058 0.015647670547529517 0.5257046864725773