BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230404.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 = 573,728 number of mapped reads = 505,035 (88.03%) number of supplementary alignments = 5,080 (0.89%) number of secondary alignments = 0 number of mapped bases = 33,905,929 bp number of sequenced bases = 33,889,076 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,429 duplication rate = 2.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8612 >>>>>>> ACTG content number of A's = 9,927,390 bp (29.29%) number of C's = 6,003,990 bp (17.72%) number of T's = 11,030,053 bp (32.55%) number of G's = 6,909,817 bp (20.39%) number of N's = 17,826 bp (0.05%) GC percentage = 38.11% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 300,770 number of insertions = 2,888 mapped reads with insertion percentage = 0.57% number of deletions = 10,165 mapped reads with deletion percentage = 1.99% homopolymer indels = 47.23% >>>>>>> Coverage mean coverageData = 0.011X std coverageData = 0.1385X There is a 1% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 2314517 0.009285902641743067 0.17899187782321407 chr2 243199373 3334428 0.013710676795207034 0.15030153987956515 chr3 198022430 2431508 0.012278952439882694 0.11888269128233925 chr4 191154276 2040788 0.010676130519832055 0.11303163103590166 chr5 180915260 1854796 0.010252291597734763 0.10817018729793604 chr6 171115067 2133711 0.012469451331249515 0.12201183066775668 chr7 159138663 1782121 0.011198541991018236 0.16126329523830293 chr8 146364022 1607637 0.01098382633950849 0.21642811831405642 chr9 141213431 1479334 0.010475873219169924 0.13517765734518988 chr10 135534747 1604404 0.01183758435023308 0.13690522469226846 chr11 135006516 1767368 0.013090982956704104 0.1400565272825221 chr12 133851895 1460653 0.010912456637240735 0.11274352038951137 chr13 115169878 1370083 0.011896192162329112 0.11664260202523423 chr14 107349540 1225983 0.011420477442194907 0.11681281975457931 chr15 102531392 871179 0.008496705087160038 0.09825482957718071 chr16 90354753 925568 0.01024371125224591 0.11850393516727104 chr17 81195210 682018 0.008399731954631314 0.1021089585801255 chr18 78077248 1085637 0.013904652479554608 0.22786812873905707 chr19 59128983 470299 0.007953781312288088 0.13227317378914422 chr20 63025520 631356 0.010017465940780814 0.10815696349813103 chr21 48129895 504557 0.010483235003940898 0.11325046572290817 chr22 51304566 252524 0.004922057034845592 0.07385300079839799 chrMT 16571 1254 0.0756743708889023 0.26925930900644 chrX 155270560 1985312 0.012786145680159846 0.12620991948891336 chrY 59373566 88894 0.001497198264965254 0.04960758965740617