BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365355.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 543,114,166 number of mapped reads = 522,632,115 (96.23%) number of supplementary alignments = 2,242,857 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 261,716,020 number of mapped paired reads (second in pair) = 260,916,095 number of mapped paired reads (both in pair) = 520,589,164 number of mapped paired reads (singletons) = 2,042,951 number of mapped bases = 54,594,080,770 bp number of sequenced bases = 54,576,049,389 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 282,521,606 duplication rate = 31.3% >>>>>>> Insert size mean insert size = 61,180.5317 std insert size = 2,405,563.3082 median insert size = 161 >>>>>>> Mapping quality mean mapping quality = 53.878 >>>>>>> ACTG content number of A's = 16,513,055,091 bp (30.26%) number of C's = 10,598,308,370 bp (19.42%) number of T's = 16,101,083,480 bp (29.5%) number of G's = 11,357,705,267 bp (20.81%) number of N's = 5,897,181 bp (0.01%) GC percentage = 40.23% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 256,864,608 number of insertions = 16,569,377 mapped reads with insertion percentage = 3.1% number of deletions = 8,497,732 mapped reads with deletion percentage = 1.58% homopolymer indels = 50.86% >>>>>>> Coverage mean coverageData = 17.6355X std coverageData = 115.4615X There is a 89.76% of reference with a coverageData >= 1X There is a 88.1% of reference with a coverageData >= 2X There is a 85.71% of reference with a coverageData >= 3X There is a 83.39% of reference with a coverageData >= 4X There is a 80.58% of reference with a coverageData >= 5X There is a 77.81% of reference with a coverageData >= 6X There is a 74.73% of reference with a coverageData >= 7X There is a 71.68% of reference with a coverageData >= 8X There is a 68.44% of reference with a coverageData >= 9X There is a 65.26% of reference with a coverageData >= 10X There is a 61.98% of reference with a coverageData >= 11X There is a 58.8% of reference with a coverageData >= 12X There is a 55.58% of reference with a coverageData >= 13X There is a 52.47% of reference with a coverageData >= 14X There is a 49.39% of reference with a coverageData >= 15X There is a 46.44% of reference with a coverageData >= 16X There is a 43.54% of reference with a coverageData >= 17X There is a 40.79% of reference with a coverageData >= 18X There is a 38.12% of reference with a coverageData >= 19X There is a 35.59% of reference with a coverageData >= 20X There is a 33.16% of reference with a coverageData >= 21X There is a 30.87% of reference with a coverageData >= 22X There is a 28.69% of reference with a coverageData >= 23X There is a 26.64% of reference with a coverageData >= 24X There is a 24.69% of reference with a coverageData >= 25X There is a 22.88% of reference with a coverageData >= 26X There is a 21.17% of reference with a coverageData >= 27X There is a 19.57% of reference with a coverageData >= 28X There is a 18.07% of reference with a coverageData >= 29X There is a 16.69% of reference with a coverageData >= 30X There is a 15.38% of reference with a coverageData >= 31X There is a 14.18% of reference with a coverageData >= 32X There is a 13.06% of reference with a coverageData >= 33X There is a 12.02% of reference with a coverageData >= 34X There is a 11.06% of reference with a coverageData >= 35X There is a 10.17% of reference with a coverageData >= 36X There is a 9.35% of reference with a coverageData >= 37X There is a 8.6% of reference with a coverageData >= 38X There is a 7.9% of reference with a coverageData >= 39X There is a 7.26% of reference with a coverageData >= 40X There is a 6.67% of reference with a coverageData >= 41X There is a 6.12% of reference with a coverageData >= 42X There is a 5.62% of reference with a coverageData >= 43X There is a 5.17% of reference with a coverageData >= 44X There is a 4.75% of reference with a coverageData >= 45X There is a 4.36% of reference with a coverageData >= 46X There is a 4.01% of reference with a coverageData >= 47X There is a 3.69% of reference with a coverageData >= 48X There is a 3.39% of reference with a coverageData >= 49X There is a 3.12% of reference with a coverageData >= 50X There is a 2.87% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4415200915 17.713901362757287 292.0021586947074 chr2 243199373 4820448230 19.820973099301536 78.87488111769207 chr3 198022430 3827807863 19.330173167756804 18.83223496052862 chr4 191154276 3904651237 20.426700980521094 96.03767996571543 chr5 180915260 3426292353 18.938658646042352 17.403630022392548 chr6 171115067 3297923704 19.27313451596872 63.1637960379098 chr7 159138663 3069176301 19.2861762386429 109.10671577373618 chr8 146364022 2815677976 19.237500702187592 37.84552463753051 chr9 141213431 2329810668 16.498506207954115 83.78863837919963 chr10 135534747 2620882197 19.33734525656362 197.6189002628337 chr11 135006516 2514409772 18.624358634660272 72.16622481966053 chr12 133851895 2481082605 18.536028981883298 33.18914771106462 chr13 115169878 1883764239 16.356396930454334 15.10007353767776 chr14 107349540 1697103605 15.809137188664247 16.60518538876821 chr15 102531392 1532706512 14.94865603697256 20.36560969358583 chr16 90354753 1450780452 16.056492921849944 43.78506976900994 chr17 81195210 1433526256 17.65530572554711 92.06227043059769 chr18 78077248 1448051147 18.546390710389794 133.29962790904747 chr19 59128983 950910356 16.0819670448247 142.79210963315546 chr20 63025520 1111181808 17.63066465774499 30.13839505212677 chr21 48129895 783249110 16.27365091903899 62.98604441307577 chr22 51304566 610138773 11.892484832636534 55.96983222320554 chrMT 16571 51822859 3127.322370406131 545.4528949837169 chrX 155270560 1547763912 9.968173696288595 34.03879997822048 chrY 59373566 569717920 9.595480924962466 199.614977810114