BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089609.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 = 17,644,889 number of mapped reads = 15,373,763 (87.13%) number of supplementary alignments = 577 (0%) number of secondary alignments = 0 number of mapped bases = 725,334,160 bp number of sequenced bases = 725,198,730 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,729,802 duplication rate = 15.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5682 >>>>>>> ACTG content number of A's = 208,002,026 bp (28.68%) number of C's = 154,329,918 bp (21.28%) number of T's = 205,890,645 bp (28.39%) number of G's = 156,962,700 bp (21.64%) number of N's = 13,441 bp (0%) GC percentage = 42.93% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 3,121,172 number of insertions = 27,230 mapped reads with insertion percentage = 0.18% number of deletions = 89,900 mapped reads with deletion percentage = 0.58% homopolymer indels = 44.49% >>>>>>> Coverage mean coverageData = 0.2343X std coverageData = 1.559X There is a 8.94% of reference with a coverageData >= 1X There is a 4.51% of reference with a coverageData >= 2X There is a 2.75% of reference with a coverageData >= 3X There is a 1.82% of reference with a coverageData >= 4X There is a 1.26% of reference with a coverageData >= 5X There is a 0.9% of reference with a coverageData >= 6X There is a 0.66% of reference with a coverageData >= 7X There is a 0.49% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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% 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 57865780 0.23215902037812777 2.347261548634963 chr2 243199373 62914812 0.2586964399780751 1.9301100433345872 chr3 198022430 47193058 0.23832178001249657 1.141616328945483 chr4 191154276 47916681 0.25067020211465213 1.3037550927695696 chr5 180915260 44035542 0.24340424351157552 1.1631794935828146 chr6 171115067 41246705 0.2410465993622876 1.2952187991656905 chr7 159138663 39074908 0.2455400043168642 1.8142217669585714 chr8 146364022 36958325 0.252509629723075 1.6316108945584225 chr9 141213431 29929417 0.2119445493821335 1.4050855730467968 chr10 135534747 33897220 0.25009985077848707 1.963601212296084 chr11 135006516 33411071 0.24747746990226754 1.5295341597960879 chr12 133851895 32106798 0.2398680870375425 1.1989906042805136 chr13 115169878 22702851 0.19712490274583777 1.030898163933692 chr14 107349540 22289992 0.2076393806624602 1.222429999240256 chr15 102531392 20071059 0.19575525708263086 1.0384696862953413 chr16 90354753 22757071 0.25186357379561425 1.36062607994535 chr17 81195210 19475878 0.23986486394948667 1.29665976459574 chr18 78077248 18897256 0.24203281345162164 2.0289333649763788 chr19 59128983 14648738 0.24774209290898846 2.2929823942059473 chr20 63025520 16092499 0.2553330619088902 1.3101288351224984 chr21 48129895 9494449 0.1972671870570256 1.2757012217330284 chr22 51304566 9004903 0.17551854936264347 1.015450868721014 chrMT 16571 246695 14.887152253937602 14.40687093603127 chrX 155270560 40724678 0.2622820320864432 1.338546181400103 chrY 59373566 2377774 0.04004768721487943 0.9083284330762162