BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080649.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 = 1,228,774 number of mapped reads = 1,082,618 (88.11%) number of supplementary alignments = 10,649 (0.87%) number of secondary alignments = 0 number of mapped bases = 70,680,564 bp number of sequenced bases = 70,645,097 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,869 duplication rate = 3.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6107 >>>>>>> ACTG content number of A's = 18,870,650 bp (26.71%) number of C's = 13,134,219 bp (18.59%) number of T's = 22,254,577 bp (31.5%) number of G's = 16,382,641 bp (23.19%) number of N's = 3,010 bp (0%) GC percentage = 41.78% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 541,808 number of insertions = 5,375 mapped reads with insertion percentage = 0.49% number of deletions = 21,435 mapped reads with deletion percentage = 1.96% homopolymer indels = 45.51% >>>>>>> Coverage mean coverageData = 0.0228X std coverageData = 0.245X There is a 1.99% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 8703532 0.03491879765467064 0.33086542354275866 chr2 243199373 4572698 0.01880226064563086 0.3156092278952337 chr3 198022430 5814533 0.029363001958919503 0.19087151200882194 chr4 191154276 2851545 0.014917505690534488 0.14148366548704333 chr5 180915260 3083258 0.01704255351372792 0.14482262049827024 chr6 171115067 4096471 0.023939861473449325 0.22609301465247705 chr7 159138663 4246292 0.026682968927544654 0.5553984761467994 chr8 146364022 7545764 0.051554773481149625 0.30187418117334197 chr9 141213431 2224972 0.01575609334214109 0.18482779610001993 chr10 135534747 3476907 0.025653251855776882 0.21062818449675696 chr11 135006516 2775019 0.020554704189240762 0.19044480354268853 chr12 133851895 2294527 0.017142282520542573 0.14732134683405756 chr13 115169878 1263485 0.010970620286669053 0.11624068371081615 chr14 107349540 1336550 0.012450449252041508 0.1309274864101245 chr15 102531392 1817957 0.017730735578036432 0.15388129854929086 chr16 90354753 1801372 0.019936660111283797 0.16301535474420253 chr17 81195210 1113306 0.013711473866500254 0.13542685837563492 chr18 78077248 2270046 0.029074359793009097 0.26524938174610085 chr19 59128983 1264361 0.02138310073758583 0.22016952745899865 chr20 63025520 1746345 0.027708537747883715 0.18729554805339757 chr21 48129895 1073064 0.02229516602934621 0.17160599651458075 chr22 51304566 674465 0.013146295789735363 0.12605208747569802 chrMT 16571 61735 3.725484279765856 2.781940315577499 chrX 155270560 4406613 0.028380222239167554 0.19937483041864365 chrY 59373566 165747 0.0027915958425000107 0.06854083676304855