BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013203.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 = 4,168,558 number of mapped reads = 3,598,109 (86.32%) number of supplementary alignments = 23,640 (0.57%) number of secondary alignments = 0 number of mapped bases = 231,477,580 bp number of sequenced bases = 231,378,394 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 254,988 duplication rate = 5.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6768 >>>>>>> ACTG content number of A's = 66,081,376 bp (28.56%) number of C's = 43,282,151 bp (18.71%) number of T's = 71,957,978 bp (31.1%) number of G's = 50,054,894 bp (21.63%) number of N's = 1,995 bp (0%) GC percentage = 40.34% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,681,453 number of insertions = 17,178 mapped reads with insertion percentage = 0.47% number of deletions = 58,664 mapped reads with deletion percentage = 1.61% homopolymer indels = 45.11% >>>>>>> Coverage mean coverageData = 0.0748X std coverageData = 0.5696X There is a 5.44% of reference with a coverageData >= 1X There is a 1.36% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% 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% 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 16083405 0.06452704083734259 0.7690772857307971 chr2 243199373 23070446 0.09486227581680484 0.9086302914854878 chr3 198022430 17546149 0.08860687650383849 0.38752839564086 chr4 191154276 16479196 0.08620887978461962 0.403872529161441 chr5 180915260 21241113 0.11740918372502132 0.4537971748135626 chr6 171115067 15005258 0.08769103891944244 0.48353052171037464 chr7 159138663 14325805 0.09002089580204654 0.903234924790005 chr8 146364022 13312536 0.0909549752602453 0.7969422488128985 chr9 141213431 10892259 0.07713330752511778 0.5110453865605936 chr10 135534747 8326295 0.06143291801031657 0.47318012147759086 chr11 135006516 7698725 0.057024840193639244 0.373359354593015 chr12 133851895 9467507 0.07073121377922965 0.35642516808946634 chr13 115169878 5977904 0.051905099699766984 0.3049980366228183 chr14 107349540 8019315 0.07470283524270342 0.3882746978645709 chr15 102531392 7579492 0.07392362331333607 0.35699058639263204 chr16 90354753 4768970 0.05278051061685709 0.3507406488422085 chr17 81195210 4491481 0.05531706858076973 0.30968700396374954 chr18 78077248 4953269 0.06344061973085936 0.9595645391608919 chr19 59128983 3349414 0.056645892252197204 0.6047133508182773 chr20 63025520 3594366 0.0570303267628732 0.31737102655881383 chr21 48129895 3058975 0.0635566522636295 0.36208347570669114 chr22 51304566 2256854 0.04398934005211154 0.26970311405197306 chrMT 16571 60286 3.6380423631645646 3.183315196900633 chrX 155270560 9400114 0.060540220889265806 0.3568379164139991 chrY 59373566 518446 0.008731932995232256 0.18450507047858805