BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779331.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 271,951,602 number of mapped reads = 267,184,282 (98.25%) number of supplementary alignments = 1,119,095 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 134,424,999 number of mapped paired reads (second in pair) = 132,759,283 number of mapped paired reads (both in pair) = 265,264,358 number of mapped paired reads (singletons) = 1,919,924 number of mapped bases = 26,676,063,393 bp number of sequenced bases = 26,669,778,677 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,633,862 duplication rate = 15.38% >>>>>>> Insert size mean insert size = 215,091.8334 std insert size = 4,465,291.6995 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 53.8544 >>>>>>> ACTG content number of A's = 8,197,524,405 bp (30.74%) number of C's = 5,168,918,596 bp (19.38%) number of T's = 7,965,704,687 bp (29.87%) number of G's = 5,330,396,008 bp (19.99%) number of N's = 7,234,981 bp (0.03%) GC percentage = 39.37% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 76,367,343 number of insertions = 2,270,484 mapped reads with insertion percentage = 0.84% number of deletions = 2,833,511 mapped reads with deletion percentage = 1.04% homopolymer indels = 47.62% >>>>>>> Coverage mean coverageData = 8.6172X std coverageData = 16.552X There is a 76.15% of reference with a coverageData >= 1X There is a 65.97% of reference with a coverageData >= 2X There is a 57.58% of reference with a coverageData >= 3X There is a 50.72% of reference with a coverageData >= 4X There is a 45% of reference with a coverageData >= 5X There is a 40.17% of reference with a coverageData >= 6X There is a 36.05% of reference with a coverageData >= 7X There is a 32.51% of reference with a coverageData >= 8X There is a 29.44% of reference with a coverageData >= 9X There is a 26.76% of reference with a coverageData >= 10X There is a 24.41% of reference with a coverageData >= 11X There is a 22.33% of reference with a coverageData >= 12X There is a 20.49% of reference with a coverageData >= 13X There is a 18.84% of reference with a coverageData >= 14X There is a 17.37% of reference with a coverageData >= 15X There is a 16.06% of reference with a coverageData >= 16X There is a 14.87% of reference with a coverageData >= 17X There is a 13.8% of reference with a coverageData >= 18X There is a 12.82% of reference with a coverageData >= 19X There is a 11.94% of reference with a coverageData >= 20X There is a 11.14% of reference with a coverageData >= 21X There is a 10.41% of reference with a coverageData >= 22X There is a 9.74% of reference with a coverageData >= 23X There is a 9.12% of reference with a coverageData >= 24X There is a 8.56% of reference with a coverageData >= 25X There is a 8.04% of reference with a coverageData >= 26X There is a 7.56% of reference with a coverageData >= 27X There is a 7.12% of reference with a coverageData >= 28X There is a 6.71% of reference with a coverageData >= 29X There is a 6.33% of reference with a coverageData >= 30X There is a 5.98% of reference with a coverageData >= 31X There is a 5.66% of reference with a coverageData >= 32X There is a 5.35% of reference with a coverageData >= 33X There is a 5.07% of reference with a coverageData >= 34X There is a 4.8% of reference with a coverageData >= 35X There is a 4.56% of reference with a coverageData >= 36X There is a 4.33% of reference with a coverageData >= 37X There is a 4.11% of reference with a coverageData >= 38X There is a 3.91% of reference with a coverageData >= 39X There is a 3.72% of reference with a coverageData >= 40X There is a 3.54% of reference with a coverageData >= 41X There is a 3.37% of reference with a coverageData >= 42X There is a 3.22% of reference with a coverageData >= 43X There is a 3.07% of reference with a coverageData >= 44X There is a 2.93% of reference with a coverageData >= 45X There is a 2.8% of reference with a coverageData >= 46X There is a 2.67% of reference with a coverageData >= 47X There is a 2.55% of reference with a coverageData >= 48X There is a 2.44% of reference with a coverageData >= 49X There is a 2.34% of reference with a coverageData >= 50X There is a 2.24% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2238531699 8.98104762996759 18.531686150905593 chr2 243199373 2337152428 9.610026535718083 15.897930602465008 chr3 198022430 1821904245 9.20049433288946 15.666587952888948 chr4 191154276 1907290744 9.977756103138388 15.841117388041509 chr5 180915260 1852679550 10.240593026812663 16.89648466600311 chr6 171115067 1693889085 9.899122939302591 15.985352185231195 chr7 159138663 1401349487 8.805839263586122 17.121499823406793 chr8 146364022 1347248708 9.20478058467128 15.023671906268978 chr9 141213431 1101052703 7.797082014103885 15.065732725387637 chr10 135534747 1442241872 10.641122693061138 30.738876634241933 chr11 135006516 1284813498 9.516677683912679 15.80791698370027 chr12 133851895 1262286327 9.430470349336481 16.259236988088556 chr13 115169878 900011113 7.814639805383835 14.483819649170217 chr14 107349540 818726528 7.626735317170432 13.4828641486122 chr15 102531392 818646356 7.984348403267557 15.872604744448001 chr16 90354753 536812789 5.941168241586583 11.25562924458473 chr17 81195210 507374768 6.248826353180194 11.947885686793628 chr18 78077248 614672307 7.87261747493969 14.596216088060535 chr19 59128983 225393738 3.811899453775486 11.098614857874885 chr20 63025520 409958250 6.5046389145222445 12.433655385071168 chr21 48129895 296243770 6.155088640854089 12.518112332394145 chr22 51304566 159208781 3.1032088060154335 7.432722242020882 chrMT 16571 1005394 60.67189668698328 23.405209978775744 chrX 155270560 1681023873 10.826417274465939 18.104152490911318 chrY 59373566 16545380 0.27866576179709335 3.045458630805114