BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716280.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 607,860 number of mapped reads = 506,425 (83.31%) number of supplementary alignments = 1,195 (0.2%) number of secondary alignments = 0 number of mapped bases = 28,051,995 bp number of sequenced bases = 28,043,955 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,343 duplication rate = 1.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.026 >>>>>>> ACTG content number of A's = 6,524,645 bp (23.27%) number of C's = 5,611,505 bp (20.01%) number of T's = 8,728,515 bp (31.12%) number of G's = 7,178,567 bp (25.6%) number of N's = 723 bp (0%) GC percentage = 45.61% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 148,232 number of insertions = 2,253 mapped reads with insertion percentage = 0.44% number of deletions = 5,058 mapped reads with deletion percentage = 0.99% homopolymer indels = 39.53% >>>>>>> Coverage mean coverageData = 0.0091X std coverageData = 0.1107X There is a 0.86% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 2680848 0.010755632179548311 0.12801781984454122 chr2 243199373 2402586 0.009879079745818259 0.15060839929188272 chr3 198022430 1875154 0.009469402026831001 0.10448051485171375 chr4 191154276 1804308 0.009439014589451298 0.10519736166658818 chr5 180915260 1728933 0.009556590195874024 0.10203693055223298 chr6 171115067 1218924 0.007123417133103773 0.09307680719163035 chr7 159138663 1651335 0.010376705251067743 0.122147257323379 chr8 146364022 1734850 0.011852981192331542 0.11903725568331709 chr9 141213431 1229349 0.0087056095960164 0.10203313700936396 chr10 135534747 1458488 0.010760989578561725 0.12839867312372405 chr11 135006516 1166749 0.008642168056540323 0.11018782664586502 chr12 133851895 1359187 0.01015440984231116 0.10594086412033484 chr13 115169878 509368 0.004422753664808084 0.06962502109245278 chr14 107349540 896025 0.008346798691452242 0.0976202669861645 chr15 102531392 564333 0.005504002130391442 0.07858782694647348 chr16 90354753 765175 0.008468563906095787 0.09994449569370482 chr17 81195210 1119003 0.01378163810402116 0.1255016442440752 chr18 78077248 757301 0.009699381310160932 0.11887057956832335 chr19 59128983 740696 0.012526784030768803 0.12794114342660443 chr20 63025520 722242 0.011459516716403132 0.11329613154535267 chr21 48129895 376013 0.007812462503813898 0.09625679221545229 chr22 51304566 299370 0.005835153151865664 0.08049681835571157 chrMT 16571 900 0.05431174944179591 0.22663182326047568 chrX 155270560 901188 0.005803984992390058 0.0857380921263559 chrY 59373566 89670 0.0015102680543055136 0.05559661233089551