BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617505.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,304,212 (94.7%) number of supplementary alignments = 162,680 (0.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,311,713 number of mapped paired reads (second in pair) = 14,992,499 number of mapped paired reads (both in pair) = 29,680,604 number of mapped paired reads (singletons) = 623,608 number of mapped bases = 2,946,894,290 bp number of sequenced bases = 2,945,155,486 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,203,570 duplication rate = 9.89% >>>>>>> Insert size mean insert size = 40,702.3826 std insert size = 1,885,310.6002 median insert size = 218 >>>>>>> Mapping quality mean mapping quality = 52.6767 >>>>>>> ACTG content number of A's = 869,460,895 bp (29.52%) number of C's = 594,396,886 bp (20.18%) number of T's = 868,865,075 bp (29.5%) number of G's = 609,663,398 bp (20.7%) number of N's = 2,769,232 bp (0.09%) GC percentage = 40.88% >>>>>>> Mismatches and indels general error rate = 0.0125 number of mismatches = 35,927,893 number of insertions = 439,246 mapped reads with insertion percentage = 1.42% number of deletions = 1,021,786 mapped reads with deletion percentage = 3.3% homopolymer indels = 47.38% >>>>>>> Coverage mean coverageData = 0.9519X std coverageData = 9.5869X There is a 38.04% of reference with a coverageData >= 1X There is a 20.47% of reference with a coverageData >= 2X There is a 11.52% of reference with a coverageData >= 3X There is a 6.83% of reference with a coverageData >= 4X There is a 4.2% of reference with a coverageData >= 5X There is a 2.69% of reference with a coverageData >= 6X There is a 1.78% of reference with a coverageData >= 7X There is a 1.21% of reference with a coverageData >= 8X There is a 0.85% of reference with a coverageData >= 9X There is a 0.61% of reference with a coverageData >= 10X There is a 0.45% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.21% 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 0.12% 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 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% 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 0.02% of reference with a coverageData >= 35X There is a 0.02% 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 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% 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 189768382 0.761355703904144 9.304242211453202 chr2 243199373 304559016 1.2523018141169302 11.252211308716362 chr3 198022430 243553420 1.2299284480046022 2.2374121197749415 chr4 191154276 152434519 0.7974423705802951 6.0448696940046025 chr5 180915260 188929427 1.0442979049970689 2.0739041215153144 chr6 171115067 138979961 0.8122017741430099 5.3481351446447905 chr7 159138663 227021551 1.4265643981186396 13.017196395159674 chr8 146364022 130950690 0.8946917979611136 3.834012752120491 chr9 141213431 121843702 0.8628336634636403 18.07045268946002 chr10 135534747 124971943 0.9220657120494717 18.487089118186073 chr11 135006516 166144702 1.2306420973043997 12.735547200252764 chr12 133851895 128668172 0.9612726962139759 2.0208044105445184 chr13 115169878 124976628 1.085150302929035 2.1277589099525573 chr14 107349540 85903424 0.800221631131349 2.2066024830343025 chr15 102531392 66549277 0.6490624549406293 1.5429162613325886 chr16 90354753 79287971 0.8775185407235854 14.707862186528168 chr17 81195210 82289248 1.0134741692274705 13.53816466680167 chr18 78077248 52779911 0.6759960468893575 16.767316939884967 chr19 59128983 35184749 0.5950508061334321 5.756033397977678 chr20 63025520 86849862 1.3780110342604075 2.7938343053002415 chr21 48129895 42475179 0.8825113580655017 3.733539632879003 chr22 51304566 22038536 0.4295628580115072 1.2439160723464064 chrMT 16571 2070626 124.95480055518678 88.50557968114788 chrX 155270560 138489265 0.891922235612469 4.0964604415233685 chrY 59373566 10174129 0.1713578901425594 13.269758881288373