BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038496.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 71,676,496 number of mapped reads = 71,159,795 (99.28%) number of supplementary alignments = 108,590 (0.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 35,793,480 number of mapped paired reads (second in pair) = 35,366,315 number of mapped paired reads (both in pair) = 70,705,742 number of mapped paired reads (singletons) = 454,053 number of mapped bases = 10,553,986,287 bp number of sequenced bases = 10,552,190,405 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,164,571 duplication rate = 35.02% >>>>>>> Insert size mean insert size = 18,358.5053 std insert size = 1,423,927.5065 median insert size = 235 >>>>>>> Mapping quality mean mapping quality = 55.8474 >>>>>>> ACTG content number of A's = 2,685,389,395 bp (25.45%) number of C's = 2,589,590,363 bp (24.54%) number of T's = 2,705,400,347 bp (25.64%) number of G's = 2,570,996,183 bp (24.36%) number of N's = 814,117 bp (0.01%) GC percentage = 48.91% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 66,074,796 number of insertions = 546,341 mapped reads with insertion percentage = 0.73% number of deletions = 644,161 mapped reads with deletion percentage = 0.88% homopolymer indels = 45.91% >>>>>>> Coverage mean coverageData = 3.4092X std coverageData = 21.3117X There is a 21.92% of reference with a coverageData >= 1X There is a 13.78% of reference with a coverageData >= 2X There is a 8.86% of reference with a coverageData >= 3X There is a 6.89% of reference with a coverageData >= 4X There is a 5.53% of reference with a coverageData >= 5X There is a 4.83% of reference with a coverageData >= 6X There is a 4.35% of reference with a coverageData >= 7X There is a 4.06% of reference with a coverageData >= 8X There is a 3.85% of reference with a coverageData >= 9X There is a 3.7% of reference with a coverageData >= 10X There is a 3.58% of reference with a coverageData >= 11X There is a 3.48% of reference with a coverageData >= 12X There is a 3.4% of reference with a coverageData >= 13X There is a 3.32% of reference with a coverageData >= 14X There is a 3.25% of reference with a coverageData >= 15X There is a 3.19% of reference with a coverageData >= 16X There is a 3.14% of reference with a coverageData >= 17X There is a 3.08% of reference with a coverageData >= 18X There is a 3.03% of reference with a coverageData >= 19X There is a 2.98% of reference with a coverageData >= 20X There is a 2.94% of reference with a coverageData >= 21X There is a 2.89% of reference with a coverageData >= 22X There is a 2.85% of reference with a coverageData >= 23X There is a 2.81% of reference with a coverageData >= 24X There is a 2.77% of reference with a coverageData >= 25X There is a 2.73% of reference with a coverageData >= 26X There is a 2.7% of reference with a coverageData >= 27X There is a 2.66% of reference with a coverageData >= 28X There is a 2.63% of reference with a coverageData >= 29X There is a 2.59% of reference with a coverageData >= 30X There is a 2.56% of reference with a coverageData >= 31X There is a 2.53% of reference with a coverageData >= 32X There is a 2.49% of reference with a coverageData >= 33X There is a 2.46% of reference with a coverageData >= 34X There is a 2.43% of reference with a coverageData >= 35X There is a 2.4% of reference with a coverageData >= 36X There is a 2.37% of reference with a coverageData >= 37X There is a 2.35% of reference with a coverageData >= 38X There is a 2.32% of reference with a coverageData >= 39X There is a 2.29% of reference with a coverageData >= 40X There is a 2.26% of reference with a coverageData >= 41X There is a 2.23% of reference with a coverageData >= 42X There is a 2.21% of reference with a coverageData >= 43X There is a 2.18% of reference with a coverageData >= 44X There is a 2.16% of reference with a coverageData >= 45X There is a 2.13% of reference with a coverageData >= 46X There is a 2.11% of reference with a coverageData >= 47X There is a 2.08% of reference with a coverageData >= 48X There is a 2.06% of reference with a coverageData >= 49X There is a 2.03% of reference with a coverageData >= 50X There is a 2.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1038391013 4.1660518591044955 23.488545496852424 chr2 243199373 798479925 3.283231840404457 21.69271880023217 chr3 198022430 626009255 3.161304782493579 20.071234573171665 chr4 191154276 440717504 2.3055592227505284 17.256718775643808 chr5 180915260 489211559 2.704092286079129 18.46717201568373 chr6 171115067 561307600 3.280293254363159 21.28938855644694 chr7 159138663 549805458 3.454882978374652 23.14132392964458 chr8 146364022 370210097 2.52937909153658 17.327946453024968 chr9 141213431 430037621 3.0453025463279055 19.910500837895423 chr10 135534747 435271841 3.2115147638118215 19.707785609624107 chr11 135006516 611055078 4.526115450605362 25.789576893106307 chr12 133851895 568962315 4.250685543152004 22.982281934793654 chr13 115169878 205797783 1.7869063211128868 14.724435978702344 chr14 107349540 350602790 3.2659924765397226 20.557097844224927 chr15 102531392 388193970 3.786098700386317 22.073752348646316 chr16 90354753 442219806 4.894261688701644 25.133770840763567 chr17 81195210 587779906 7.239095828436185 30.76974507506373 chr18 78077248 172517836 2.2095788519595363 16.13056677302757 chr19 59128983 649838871 10.990191916542857 39.31997653429541 chr20 63025520 254865924 4.0438527758279506 23.162424210908203 chr21 48129895 117583149 2.443037721150233 24.227358925913943 chr22 51304566 225351004 4.392416144793039 22.975107770245263 chrMT 16571 241682 14.584635809546798 7.940699080494518 chrX 155270560 218680430 1.4083830830519322 10.089797392827636 chrY 59373566 20853870 0.3512315564808757 5.03518235088603