BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472421.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 32,456,550 number of mapped reads = 32,087,014 (98.86%) number of supplementary alignments = 45,380 (0.14%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,146,565 number of mapped paired reads (second in pair) = 15,940,449 number of mapped paired reads (both in pair) = 31,824,452 number of mapped paired reads (singletons) = 262,562 number of mapped bases = 3,155,424,418 bp number of sequenced bases = 3,154,965,703 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,023,302 duplication rate = 51.49% >>>>>>> Insert size mean insert size = 45,447.5084 std insert size = 2,144,334.8724 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 54.8468 >>>>>>> ACTG content number of A's = 887,126,901 bp (28.12%) number of C's = 690,866,568 bp (21.9%) number of T's = 892,427,210 bp (28.29%) number of G's = 684,123,316 bp (21.68%) number of N's = 421,708 bp (0.01%) GC percentage = 43.58% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 16,083,238 number of insertions = 155,290 mapped reads with insertion percentage = 0.48% number of deletions = 194,326 mapped reads with deletion percentage = 0.6% homopolymer indels = 45.64% >>>>>>> Coverage mean coverageData = 1.0193X std coverageData = 19.1404X There is a 8.78% of reference with a coverageData >= 1X There is a 3.52% of reference with a coverageData >= 2X There is a 1.39% of reference with a coverageData >= 3X There is a 1.03% of reference with a coverageData >= 4X There is a 0.78% of reference with a coverageData >= 5X There is a 0.72% of reference with a coverageData >= 6X There is a 0.67% of reference with a coverageData >= 7X There is a 0.64% of reference with a coverageData >= 8X There is a 0.62% of reference with a coverageData >= 9X There is a 0.61% of reference with a coverageData >= 10X There is a 0.59% of reference with a coverageData >= 11X There is a 0.58% of reference with a coverageData >= 12X There is a 0.57% of reference with a coverageData >= 13X There is a 0.56% of reference with a coverageData >= 14X There is a 0.55% of reference with a coverageData >= 15X There is a 0.54% of reference with a coverageData >= 16X There is a 0.53% of reference with a coverageData >= 17X There is a 0.52% of reference with a coverageData >= 18X There is a 0.51% of reference with a coverageData >= 19X There is a 0.5% of reference with a coverageData >= 20X There is a 0.5% of reference with a coverageData >= 21X There is a 0.49% of reference with a coverageData >= 22X There is a 0.48% of reference with a coverageData >= 23X There is a 0.48% of reference with a coverageData >= 24X There is a 0.47% of reference with a coverageData >= 25X There is a 0.47% of reference with a coverageData >= 26X There is a 0.46% of reference with a coverageData >= 27X There is a 0.45% of reference with a coverageData >= 28X There is a 0.45% of reference with a coverageData >= 29X There is a 0.44% of reference with a coverageData >= 30X There is a 0.44% of reference with a coverageData >= 31X There is a 0.43% of reference with a coverageData >= 32X There is a 0.43% of reference with a coverageData >= 33X There is a 0.43% of reference with a coverageData >= 34X There is a 0.42% of reference with a coverageData >= 35X There is a 0.42% of reference with a coverageData >= 36X There is a 0.41% of reference with a coverageData >= 37X There is a 0.41% of reference with a coverageData >= 38X There is a 0.4% of reference with a coverageData >= 39X There is a 0.4% of reference with a coverageData >= 40X There is a 0.4% of reference with a coverageData >= 41X There is a 0.39% of reference with a coverageData >= 42X There is a 0.39% of reference with a coverageData >= 43X There is a 0.39% of reference with a coverageData >= 44X There is a 0.38% of reference with a coverageData >= 45X There is a 0.38% of reference with a coverageData >= 46X There is a 0.38% of reference with a coverageData >= 47X There is a 0.37% of reference with a coverageData >= 48X There is a 0.37% of reference with a coverageData >= 49X There is a 0.37% of reference with a coverageData >= 50X There is a 0.36% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 344726326 1.3830510215659604 23.2045411004058 chr2 243199373 235025413 0.9663898804541737 19.63348175326253 chr3 198022430 284488763 1.4366491866603193 21.716094069263043 chr4 191154276 118759652 0.6212764604857701 15.040238021750891 chr5 180915260 153452170 0.8481991513595923 17.167132337787827 chr6 171115067 220052544 1.285991630415573 19.931735934563722 chr7 159138663 185166809 1.1635563948403915 22.38186973032001 chr8 146364022 179479248 1.2262525007682556 20.638302502063407 chr9 141213431 151829959 1.0751807241338114 17.494105979535323 chr10 135534747 85461536 0.6305507472559786 13.52616673375092 chr11 135006516 126249988 0.9351399602075503 19.009057872000312 chr12 133851895 139608812 1.0430096040104624 16.513572761254775 chr13 115169878 85592647 0.7431860525197396 18.747836311193215 chr14 107349540 85437104 0.7958776907660713 16.032195256390466 chr15 102531392 80284843 0.7830269484686212 17.860964653124547 chr16 90354753 154256346 1.707230011463813 29.486060456822052 chr17 81195210 159714717 1.9670460486523773 29.070411632839406 chr18 78077248 52335747 0.6703072705636346 13.20100229341698 chr19 59128983 77992665 1.3190259842622356 17.3066173617077 chr20 63025520 60767192 0.9641680385976982 17.577353375635518 chr21 48129895 26203990 0.5444431158638513 20.50471464099668 chr22 51304566 50673007 0.9876900040436947 19.967919399898534 chrMT 16571 720448 43.47643473538109 10.917399795118852 chrX 155270560 90498468 0.5828437019870347 8.960711522983264 chrY 59373566 6646024 0.11193573921431635 3.0587131926713917