BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504417.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 2,217,180 number of mapped reads = 1,942,022 (87.59%) number of secondary alignments = 0 number of mapped bases = 62,138,220 bp number of sequenced bases = 62,138,220 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,143 duplication rate = 3.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 8.2259 >>>>>>> ACTG content number of A's = 18,030,027 bp (29.02%) number of C's = 12,327,723 bp (19.84%) number of T's = 19,336,989 bp (31.12%) number of G's = 12,443,316 bp (20.03%) number of N's = 165 bp (0%) GC percentage = 39.86% >>>>>>> Mismatches and indels general error rate = 0.0005 number of mismatches = 31,841 >>>>>>> Coverage mean coverageData = 0.0201X std coverageData = 0.4275X There is a 1.47% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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% 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 4885176 0.019599453675985024 0.22820804597973207 chr2 243199373 5050480 0.020766829855272693 0.2030945969481893 chr3 198022430 4373128 0.022084003312150043 0.2304400350934496 chr4 191154276 4358174 0.022799249335128658 0.2062863083966194 chr5 180915260 4412928 0.024392237559175495 0.2934795209427658 chr6 171115067 3820260 0.022325678661599097 0.28118747954397866 chr7 159138663 3357986 0.02110100673649621 0.2616731657798568 chr8 146364022 3685812 0.025182500109214 0.3362133536933325 chr9 141213431 2252892 0.015953808246469133 0.16461978291575483 chr10 135534747 2985636 0.02202856511769635 0.3245152332591856 chr11 135006516 3297246 0.024422865634129837 0.24721496983719854 chr12 133851895 3614946 0.027007058809290673 0.45626641289174663 chr13 115169878 2046038 0.01776539174592162 0.20787739683746137 chr14 107349540 3812728 0.035516947720502574 1.8551868167648708 chr15 102531392 1726244 0.016836248551077897 0.18195666043927422 chr16 90354753 1366208 0.015120488459527967 0.24161540824479905 chr17 81195210 1027312 0.012652371981056518 0.15190865326308992 chr18 78077248 1595056 0.020429203652259875 0.2970057420628634 chr19 59128983 676750 0.011445317772504222 0.18117416627854588 chr20 63025520 1248686 0.01981238710922179 0.4692682368621251 chr21 48129895 542056 0.011262355756230094 0.1250468280739586 chr22 51304566 431176 0.008404242226705515 0.11708726983055595 chrMT 16571 32 0.001931084424597188 0.04390165529387549 chrX 155270560 842622 0.005426798228846473 0.09351195722237918 chrY 59373566 728648 0.012272262710311184 0.21836298961038708