BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237573.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 = 2,133,192 number of mapped reads = 1,549,827 (72.65%) number of supplementary alignments = 7,221 (0.34%) number of secondary alignments = 0 number of mapped bases = 94,110,586 bp number of sequenced bases = 94,051,228 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 204,393 duplication rate = 10.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5971 >>>>>>> ACTG content number of A's = 24,768,185 bp (26.33%) number of C's = 16,064,528 bp (17.08%) number of T's = 31,129,458 bp (33.1%) number of G's = 21,931,699 bp (23.32%) number of N's = 157,358 bp (0.17%) GC percentage = 40.4% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 1,001,416 number of insertions = 7,920 mapped reads with insertion percentage = 0.51% number of deletions = 37,632 mapped reads with deletion percentage = 2.4% homopolymer indels = 49.05% >>>>>>> Coverage mean coverageData = 0.0304X std coverageData = 0.2997X There is a 1.98% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.09% 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 7853979 0.03151036883474806 0.36462399737534934 chr2 243199373 8378507 0.03445118668130777 0.35114531894010087 chr3 198022430 6936137 0.03502702698881132 0.2764899203521833 chr4 191154276 6093922 0.03187960074719961 0.2649486914345167 chr5 180915260 5603178 0.030971284567150387 0.2543676630756319 chr6 171115067 5293244 0.03093382770320278 0.2761063614762243 chr7 159138663 5452824 0.034264608594832796 0.3894610227561296 chr8 146364022 4990163 0.034094191535676714 0.375654402136264 chr9 141213431 3881968 0.02749007635116521 0.28836284472193985 chr10 135534747 4294041 0.031682215041136275 0.2984736397618121 chr11 135006516 4065665 0.030114583506473124 0.29720006383576875 chr12 133851895 4970913 0.037137412212206636 0.28673587734770245 chr13 115169878 3256152 0.028272600931295595 0.25061283593203587 chr14 107349540 2688189 0.02504145802580989 0.23627449530841424 chr15 102531392 2569879 0.02506431396152312 0.23066889503171814 chr16 90354753 2255561 0.024963390691799026 0.24071381548725077 chr17 81195210 2025568 0.02494689033995971 0.24004003495202025 chr18 78077248 2460522 0.031513943729164225 0.42237861785496356 chr19 59128983 1406862 0.023793103290817633 0.2830893702332066 chr20 63025520 1794432 0.02847151439607321 0.2522379861672763 chr21 48129895 1166035 0.024226834486133827 0.2329540247298998 chr22 51304566 842001 0.01641181410637018 0.18006644278508072 chrMT 16571 123001 7.422666103433709 5.49456336168034 chrX 155270560 5420304 0.03490876828163691 0.28086807899279775 chrY 59373566 287539 0.004842879068439312 0.11058877441880688