BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089397.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 23,259,582 number of mapped reads = 21,668,252 (93.16%) number of supplementary alignments = 147,303 (0.63%) number of secondary alignments = 0 number of mapped bases = 1,419,416,664 bp number of sequenced bases = 1,418,955,727 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,331,391 duplication rate = 13.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.484 >>>>>>> ACTG content number of A's = 378,775,624 bp (26.69%) number of C's = 275,483,041 bp (19.41%) number of T's = 431,752,866 bp (30.43%) number of G's = 332,854,697 bp (23.46%) number of N's = 89,499 bp (0.01%) GC percentage = 42.87% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 8,735,148 number of insertions = 91,277 mapped reads with insertion percentage = 0.42% number of deletions = 263,618 mapped reads with deletion percentage = 1.2% homopolymer indels = 44.51% >>>>>>> Coverage mean coverageData = 0.4585X std coverageData = 2.8197X There is a 16.66% of reference with a coverageData >= 1X There is a 9.23% of reference with a coverageData >= 2X There is a 5.65% of reference with a coverageData >= 3X There is a 3.67% of reference with a coverageData >= 4X There is a 2.48% of reference with a coverageData >= 5X There is a 1.73% of reference with a coverageData >= 6X There is a 1.24% of reference with a coverageData >= 7X There is a 0.91% of reference with a coverageData >= 8X There is a 0.68% of reference with a coverageData >= 9X There is a 0.52% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 116341974 0.46676703766366945 4.167174971466691 chr2 243199373 120755461 0.4965286690932382 3.862359020226247 chr3 198022430 94214659 0.4757777136660731 1.609609195220577 chr4 191154276 91009760 0.4761063257617109 2.2047308148466738 chr5 180915260 85414241 0.47212292097416214 1.6374339584486854 chr6 171115067 82403428 0.48156734205059804 2.081751490405384 chr7 159138663 78704584 0.49456607537289665 3.8013384219603363 chr8 146364022 69359136 0.4738810470786325 3.11035240127559 chr9 141213431 59628346 0.42225690274461214 2.7352194035209374 chr10 135534747 68213864 0.5032942880691694 3.5797444512951575 chr11 135006516 64834605 0.4802331540797631 3.0803453394151443 chr12 133851895 65493317 0.48929689788852077 1.7386821229925034 chr13 115169878 43975183 0.3818288580630432 1.4415079464382745 chr14 107349540 42262782 0.3936931821039941 2.094785068080405 chr15 102531392 41182256 0.4016550950561561 1.4899451087405624 chr16 90354753 41870016 0.46339583264645745 2.0550614130944047 chr17 81195210 38433106 0.47334203581713746 2.1741571215936677 chr18 78077248 36767057 0.470906159499884 4.71704444031959 chr19 59128983 28584142 0.48342015285464995 3.859493643391433 chr20 63025520 31303405 0.49667825033415036 1.8187530077514966 chr21 48129895 18387306 0.3820350324886435 2.1078154976767665 chr22 51304566 16211695 0.31598932149625825 1.3136203016010952 chrMT 16571 362409 21.87007422605757 16.991448929525003 chrX 155270560 79843253 0.5142201651105013 2.1859735699026244 chrY 59373566 3860679 0.0650235325262424 1.7976606919460123