BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013224.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 = 2,004,263 number of mapped reads = 1,703,319 (84.98%) number of supplementary alignments = 13,850 (0.69%) number of secondary alignments = 0 number of mapped bases = 110,856,847 bp number of sequenced bases = 110,807,110 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,104 duplication rate = 5.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6342 >>>>>>> ACTG content number of A's = 30,044,262 bp (27.11%) number of C's = 20,079,970 bp (18.12%) number of T's = 35,645,274 bp (32.17%) number of G's = 25,036,199 bp (22.59%) number of N's = 1,405 bp (0%) GC percentage = 40.72% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 817,590 number of insertions = 7,743 mapped reads with insertion percentage = 0.45% number of deletions = 28,658 mapped reads with deletion percentage = 1.67% homopolymer indels = 46.47% >>>>>>> Coverage mean coverageData = 0.0358X std coverageData = 0.3752X There is a 2.64% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 10579166 0.04244389024009693 0.57225906070234 chr2 243199373 13850374 0.056950697812859906 0.43728154552328563 chr3 198022430 6378397 0.032210477368649605 0.23348559423755363 chr4 191154276 7383749 0.038627171489483185 0.2658877744889993 chr5 180915260 5644390 0.03119908182427508 0.23101732188120983 chr6 171115067 6353899 0.03713231751824636 0.29707536485098607 chr7 159138663 7264246 0.04564727303257537 0.7621550567887991 chr8 146364022 4568382 0.03121246558802545 0.3550360499959628 chr9 141213431 6004707 0.04252220881170998 0.36913249271247806 chr10 135534747 3770816 0.027821765882663285 0.34551833713717967 chr11 135006516 4929871 0.03651580046699376 0.307845777928792 chr12 133851895 5013068 0.03745234985279813 0.25663330480110347 chr13 115169878 3909167 0.03394261648866208 0.23857340321168044 chr14 107349540 1805050 0.01681469711002022 0.20407881545280465 chr15 102531392 2891462 0.028200748508320262 0.21659136799702186 chr16 90354753 4885377 0.054068843506218205 0.3213554623523353 chr17 81195210 3245245 0.039968429172114954 0.34387568875466473 chr18 78077248 1581336 0.020253480245615213 0.5688005768596001 chr19 59128983 1470824 0.02487484014396121 0.4577407276706508 chr20 63025520 2345069 0.037208245167989096 0.261218116695644 chr21 48129895 1028226 0.02136356208547723 0.21140123829298377 chr22 51304566 914927 0.01783324704471723 0.16841846843261601 chrMT 16571 35659 2.1518918592722227 2.3810469447822493 chrX 155270560 4789159 0.030843960374716237 0.2436230261534198 chrY 59373566 214281 0.003609030321675474 0.10220927115450525