BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080709.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,196,302 number of mapped reads = 2,001,336 (91.12%) number of supplementary alignments = 11,841 (0.54%) number of secondary alignments = 0 number of mapped bases = 136,106,740 bp number of sequenced bases = 136,055,839 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,036 duplication rate = 4.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4451 >>>>>>> ACTG content number of A's = 38,240,558 bp (28.11%) number of C's = 25,224,829 bp (18.54%) number of T's = 43,173,653 bp (31.73%) number of G's = 29,414,707 bp (21.62%) number of N's = 2,092 bp (0%) GC percentage = 40.16% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,101,828 number of insertions = 9,644 mapped reads with insertion percentage = 0.48% number of deletions = 29,080 mapped reads with deletion percentage = 1.44% homopolymer indels = 48.15% >>>>>>> Coverage mean coverageData = 0.044X std coverageData = 0.3675X There is a 3.68% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 16451990 0.06600581348200532 0.5312614911847109 chr2 243199373 8903712 0.03661075228183257 0.3606414294956423 chr3 198022430 8467081 0.042758191584660384 0.23585358238777454 chr4 191154276 5833234 0.03051584365290369 0.20932303937498897 chr5 180915260 6358052 0.035143812633605366 0.2131758151213907 chr6 171115067 7991124 0.046700294369752954 0.3326111194921106 chr7 159138663 8694307 0.05463353050791937 0.8863635018723826 chr8 146364022 16130154 0.11020573074986967 0.4963218787722148 chr9 141213431 4263387 0.030191087135330634 0.26724078587134764 chr10 135534747 6672696 0.049232364007733016 0.3442479081698896 chr11 135006516 5708744 0.04228495163892682 0.2669098473082155 chr12 133851895 4354640 0.03253327119500251 0.20699641686464415 chr13 115169878 2810652 0.024404401991291506 0.1781746860847529 chr14 107349540 2772500 0.025826845648337197 0.18971762398288924 chr15 102531392 2430737 0.02370724665476111 0.17650307421381686 chr16 90354753 3370292 0.03730066087392215 0.2399347592193956 chr17 81195210 2116953 0.02607238776770206 0.1921602776541288 chr18 78077248 4348288 0.0556921268536514 0.4465187414226617 chr19 59128983 2294433 0.03880386374986358 0.3496570464387551 chr20 63025520 3405954 0.05404087106302336 0.27153157118364973 chr21 48129895 1969301 0.0409163784795292 0.23953889019712596 chr22 51304566 1248707 0.024339100734230946 0.17592455362911705 chrMT 16571 86854 5.24132520668638 3.4024164184429693 chrX 155270560 9130858 0.058806112375713725 0.297054739265943 chrY 59373566 292090 0.0049195293407170455 0.10458295702223105