BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008726.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 = 2,583,514 number of mapped reads = 2,380,258 (92.13%) number of supplementary alignments = 16,098 (0.62%) number of secondary alignments = 0 number of mapped bases = 161,022,856 bp number of sequenced bases = 160,924,075 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,643 duplication rate = 2.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4189 >>>>>>> ACTG content number of A's = 45,385,724 bp (28.2%) number of C's = 29,524,288 bp (18.35%) number of T's = 50,966,620 bp (31.67%) number of G's = 34,904,001 bp (21.69%) number of N's = 143,442 bp (0.09%) GC percentage = 40.04% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,450,036 number of insertions = 13,725 mapped reads with insertion percentage = 0.57% number of deletions = 59,065 mapped reads with deletion percentage = 2.45% homopolymer indels = 45.52% >>>>>>> Coverage mean coverageData = 0.052X std coverageData = 0.5047X There is a 4.37% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 0.01% 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 14635529 0.058718124517731896 0.9125205951617035 chr2 243199373 14195431 0.05836952137208018 0.6216101964943377 chr3 198022430 11867867 0.059931932963351676 0.28807292343117 chr4 191154276 7732966 0.040454057119810385 0.2540991299036615 chr5 180915260 7967214 0.0440383746512041 0.24064709351904895 chr6 171115067 8693239 0.05080346898967114 0.29470231202546254 chr7 159138663 7183707 0.045141179802421744 0.49944605213270177 chr8 146364022 13822640 0.09444014868626663 0.9564572267161688 chr9 141213431 5356852 0.037934436987088004 0.44698096308544083 chr10 135534747 9482262 0.06996185266055796 0.5365234601707095 chr11 135006516 7285974 0.05396757294292373 0.5289180272133497 chr12 133851895 7116266 0.05316522414568729 0.2696622525724386 chr13 115169878 3808273 0.03306657145195552 0.2052307385691941 chr14 107349540 4676117 0.04355973020471257 0.25181076690386806 chr15 102531392 4495478 0.043844893864310355 0.2446373514607398 chr16 90354753 3860402 0.04272494663341064 0.2978965058266093 chr17 81195210 4391268 0.054082845527463994 0.3605306184775813 chr18 78077248 2320321 0.029718273369471217 0.8179937261656158 chr19 59128983 3365987 0.05692617781029652 0.603516754192466 chr20 63025520 3930972 0.06237111570043373 0.29406662370697506 chr21 48129895 1721587 0.03576959808451691 0.2383986572438608 chr22 51304566 1982357 0.03863899755043245 0.21956338137324063 chrMT 16571 115417 6.964999094804176 5.3876357292826125 chrX 155270560 10534940 0.06784892126363169 0.3445991808404757 chrY 59373566 479790 0.00808086884995252 0.23473466098302392