BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089715.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 = 26,254,261 number of mapped reads = 23,379,586 (89.05%) number of supplementary alignments = 180,730 (0.69%) number of secondary alignments = 0 number of mapped bases = 1,588,688,310 bp number of sequenced bases = 1,588,137,024 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,373,372 duplication rate = 14.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5545 >>>>>>> ACTG content number of A's = 438,834,478 bp (27.63%) number of C's = 298,834,869 bp (18.82%) number of T's = 493,335,562 bp (31.06%) number of G's = 356,034,612 bp (22.42%) number of N's = 1,097,503 bp (0.07%) GC percentage = 41.24% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 11,509,325 number of insertions = 104,476 mapped reads with insertion percentage = 0.44% number of deletions = 311,509 mapped reads with deletion percentage = 1.32% homopolymer indels = 47.58% >>>>>>> Coverage mean coverageData = 0.5132X std coverageData = 3.5158X There is a 11.73% of reference with a coverageData >= 1X There is a 8.04% of reference with a coverageData >= 2X There is a 6.01% of reference with a coverageData >= 3X There is a 4.64% of reference with a coverageData >= 4X There is a 3.66% of reference with a coverageData >= 5X There is a 2.91% of reference with a coverageData >= 6X There is a 2.34% of reference with a coverageData >= 7X There is a 1.9% of reference with a coverageData >= 8X There is a 1.55% of reference with a coverageData >= 9X There is a 1.27% of reference with a coverageData >= 10X There is a 1.04% of reference with a coverageData >= 11X There is a 0.86% of reference with a coverageData >= 12X There is a 0.71% of reference with a coverageData >= 13X There is a 0.59% of reference with a coverageData >= 14X There is a 0.49% of reference with a coverageData >= 15X There is a 0.41% of reference with a coverageData >= 16X There is a 0.34% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.18% of reference with a coverageData >= 21X There is a 0.15% of reference with a coverageData >= 22X There is a 0.13% of reference with a coverageData >= 23X There is a 0.11% of reference with a coverageData >= 24X There is a 0.1% of reference with a coverageData >= 25X There is a 0.09% of reference with a coverageData >= 26X There is a 0.08% of reference with a coverageData >= 27X There is a 0.07% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% 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 128666434 0.5162130930056941 6.157712046788913 chr2 243199373 141468204 0.5816964174492342 3.987789449311112 chr3 198022430 103671575 0.5235345056618081 2.203716059904364 chr4 191154276 108665264 0.5684689156521929 2.5358706681847143 chr5 180915260 95936610 0.5302847863690437 2.2027146876674424 chr6 171115067 89748043 0.5244894244175471 2.446233824308905 chr7 159138663 80988171 0.508915743498486 3.8656093876991853 chr8 146364022 79590819 0.5437867715878975 6.521251095676271 chr9 141213431 67176234 0.47570711598955484 3.0145184322500502 chr10 135534747 79672663 0.5878393899979022 3.1327934545343825 chr11 135006516 75505117 0.5592701688561462 2.825091732793142 chr12 133851895 73267989 0.5473810363312376 2.3180198707781994 chr13 115169878 48802996 0.4237479178366413 1.9410537002112265 chr14 107349540 50152793 0.46719150356862266 2.22902894033705 chr15 102531392 43977601 0.42891840383869945 2.028659596872915 chr16 90354753 42422060 0.4695055721086416 2.2428858729783094 chr17 81195210 37649877 0.4636957894437369 2.5803482718074453 chr18 78077248 41587293 0.5326429153855423 5.603201099577826 chr19 59128983 25312739 0.4280935966715342 3.8372846564433716 chr20 63025520 30530611 0.48441664582854693 2.2593573447434383 chr21 48129895 22757721 0.472839614547258 2.382376733102365 chr22 51304566 16092631 0.3136685923822063 1.731272946052234 chrMT 16571 576449 34.78661517108201 25.502870411082448 chrX 155270560 99964174 0.6438063596859572 2.5857820271749703 chrY 59373566 4504242 0.07586275009993504 2.2356256034012687