BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234128.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 = 5,979,702 number of mapped reads = 5,610,258 (93.82%) number of supplementary alignments = 56,241 (0.94%) number of secondary alignments = 0 number of mapped bases = 384,322,589 bp number of sequenced bases = 384,185,984 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 932,289 duplication rate = 7.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2254 >>>>>>> ACTG content number of A's = 98,385,362 bp (25.61%) number of C's = 67,932,443 bp (17.68%) number of T's = 106,309,383 bp (27.67%) number of G's = 111,476,086 bp (29.02%) number of N's = 82,710 bp (0.02%) GC percentage = 46.7% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 2,317,251 number of insertions = 23,106 mapped reads with insertion percentage = 0.41% number of deletions = 83,762 mapped reads with deletion percentage = 1.48% homopolymer indels = 46.7% >>>>>>> Coverage mean coverageData = 0.1241X std coverageData = 69.9064X There is a 6.23% of reference with a coverageData >= 1X There is a 2.65% of reference with a coverageData >= 2X There is a 1.18% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.26% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 33763019 0.13545811386363607 1.37761403605444 chr2 243199373 59782035 0.24581492239291258 249.39455337832973 chr3 198022430 27412062 0.1384290759385187 0.6024770413773326 chr4 191154276 27129476 0.1419245050003485 0.6155183534348927 chr5 180915260 16343373 0.0903371722208508 0.48173976621604575 chr6 171115067 14336016 0.08377997479321911 0.5128783800318178 chr7 159138663 18483932 0.11614985102645986 1.3815144284315488 chr8 146364022 23939252 0.16355967588810863 1.0832484490320449 chr9 141213431 12474547 0.08833824737251798 0.6624460116066068 chr10 135534747 19489197 0.14379483808679702 0.7830605689296982 chr11 135006516 17094309 0.12661839966302071 0.8881668096065188 chr12 133851895 17458798 0.13043370062112308 0.5924710351413862 chr13 115169878 12030693 0.10446041281731669 0.5189422956467654 chr14 107349540 9858081 0.09183160915268011 0.6471481800603194 chr15 102531392 6854507 0.0668527644684664 0.41560646056574996 chr16 90354753 9054597 0.10021162915469428 0.5430486142312929 chr17 81195210 5704591 0.0702577282576152 0.5040483060861026 chr18 78077248 7911333 0.10132699605395928 1.2695595549325447 chr19 59128983 6087072 0.10294565695472896 0.980547507612811 chr20 63025520 6493983 0.10303735693097019 0.5449595523842147 chr21 48129895 3198126 0.06644780754248476 0.4414933790426079 chr22 51304566 3740364 0.07290508996801572 0.43948112697742486 chrMT 16571 23733 1.432200832780158 1.9826823424981568 chrX 155270560 24827128 0.1598959133012723 0.7017688126362135 chrY 59373566 832365 0.014019117531192248 0.19511547403460686