BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084281.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 = 3,194,431 number of mapped reads = 2,880,185 (90.16%) number of supplementary alignments = 18,923 (0.59%) number of secondary alignments = 0 number of mapped bases = 187,504,339 bp number of sequenced bases = 187,444,818 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,941 duplication rate = 3.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6066 >>>>>>> ACTG content number of A's = 52,614,354 bp (28.07%) number of C's = 36,276,546 bp (19.35%) number of T's = 57,196,901 bp (30.51%) number of G's = 41,120,084 bp (21.94%) number of N's = 236,933 bp (0.13%) GC percentage = 41.29% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 1,927,206 number of insertions = 13,722 mapped reads with insertion percentage = 0.47% number of deletions = 36,701 mapped reads with deletion percentage = 1.26% homopolymer indels = 45.96% >>>>>>> Coverage mean coverageData = 0.0606X std coverageData = 0.3742X There is a 4.93% of reference with a coverageData >= 1X There is a 0.82% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 19115731 0.0766928119308477 0.552924146409189 chr2 243199373 17087321 0.07026054709442035 0.44359737535481353 chr3 198022430 13043523 0.06586891697066842 0.305336988611806 chr4 191154276 9316706 0.048739197442802695 0.2707283825858162 chr5 180915260 9646607 0.053321134988834 0.27170266533365456 chr6 171115067 9086391 0.05310105743055344 0.3103479332611546 chr7 159138663 10131035 0.06366168226510738 0.5574737995082539 chr8 146364022 9050713 0.06183700663814773 0.3565341650710024 chr9 141213431 7198349 0.05097496002345556 0.3139214151105825 chr10 135534747 13160755 0.0971024426673405 0.5107086728468265 chr11 135006516 10357458 0.07671820817892967 0.3828199717222691 chr12 133851895 9497095 0.07095226406768466 0.3165207710712228 chr13 115169878 4817717 0.04183139796327647 0.241898155295773 chr14 107349540 5184983 0.04830000203074927 0.2783002974837289 chr15 102531392 4153575 0.04051027611133964 0.24616390895723222 chr16 90354753 3821460 0.042293956578023074 0.2616282938748917 chr17 81195210 4852717 0.05976605023867787 0.3066257503666508 chr18 78077248 5207813 0.06670077562159978 0.48448731482855056 chr19 59128983 3784125 0.06399780290488 0.4377890003389354 chr20 63025520 3974673 0.06306450149082467 0.3021526775332993 chr21 48129895 1847622 0.03838824082205041 0.23893158552268515 chr22 51304566 1360392 0.026516002493813123 0.18992205141658447 chrMT 16571 27235 1.6435338844970129 1.6913168014963986 chrX 155270560 11392940 0.07337475951654969 0.3561957775275609 chrY 59373566 387403 0.006524839690444061 0.1292263655158703