BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524975.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 3,103,553 number of mapped reads = 2,827,244 (91.1%) number of supplementary alignments = 6,280 (0.2%) number of secondary alignments = 0 number of mapped bases = 163,978,262 bp number of sequenced bases = 163,926,258 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 169,594 duplication rate = 4.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.743 >>>>>>> ACTG content number of A's = 40,422,267 bp (24.66%) number of C's = 32,908,398 bp (20.08%) number of T's = 52,880,478 bp (32.26%) number of G's = 37,713,257 bp (23.01%) number of N's = 1,858 bp (0%) GC percentage = 43.08% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 805,659 number of insertions = 13,070 mapped reads with insertion percentage = 0.46% number of deletions = 30,426 mapped reads with deletion percentage = 1.07% homopolymer indels = 41.8% >>>>>>> Coverage mean coverageData = 0.053X std coverageData = 0.4127X There is a 4.41% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% 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 13023734 0.052251560889792124 0.7472228677184315 chr2 243199373 13990551 0.057527084989647564 0.4892681727354749 chr3 198022430 11001003 0.055554327860737794 0.2810089267212115 chr4 191154276 10671484 0.055826551324439116 0.3296202181976664 chr5 180915260 9733890 0.05380358738118609 0.2745046518438052 chr6 171115067 9465173 0.05531466729344179 0.3576229451288604 chr7 159138663 8903228 0.05594635415530668 0.5112871191441638 chr8 146364022 8014293 0.05475589486055528 0.43004575152688845 chr9 141213431 6873101 0.04867172301762146 0.35108787250806467 chr10 135534747 7740494 0.05711077174918104 0.4265152415585791 chr11 135006516 7376460 0.05463780725961405 0.40552088096438477 chr12 133851895 7322923 0.05470914700161698 0.27995594311575467 chr13 115169878 5252627 0.04560764577696262 0.2528993850754599 chr14 107349540 5050709 0.04704919089546169 0.2657972240117245 chr15 102531392 4837183 0.04717758050139415 0.28170801472868756 chr16 90354753 4796927 0.053089924334141 0.2920860113910194 chr17 81195210 4537384 0.05588240981210591 0.3262197916526576 chr18 78077248 4500568 0.05764250297346546 0.6044150399467729 chr19 59128983 3239025 0.05477897362110896 0.5031934205373522 chr20 63025520 3613128 0.05732801569903747 0.29105855603286923 chr21 48129895 2230870 0.04635102569826924 0.28643787473739896 chr22 51304566 1993487 0.03885593730585305 0.23001611708088768 chrMT 16571 8837 0.5332810331301672 0.8864888996535338 chrX 155270560 9310221 0.059961276625781476 0.32710102962883963 chrY 59373566 490962 0.008269033394423371 0.21636889636474102