- Flaviviridae
- Denguevirus
Pair Frequencies
Genera
ii(Identical Pairs)
si(Transitionsal Pairs)
sv(Transversional Pairs)
R(si/sv)
Flavivirus
3986
2059
2923
0.96
Hepacivirus
5799
1348
1798
0.96
Orthoflavivirus
5553
1924
2777
0.95
Pegivirus
4327
1636
2602
0.94
Pestivirus
7632
2018
2101
0.99
1. ii (Identical Pairs): Base pairs in DNA that are the same when two sequences are compared. They indicate the degree of similarity or genetic relationship between the sequences.
2. si (Transitional Pairs): Substitutions between purines (A and G) or between pyrimidines (C and T) in DNA. These mutations are more common because of the chemical structure similarities between purines and between pyrimidines.
3. sv (Transversional Pairs): Substitutions between a purine and a pyrimidine (e.g., A to C or T, G to C or T) in DNA. These are less common due to the more significant chemical structure changes involved.
4. R (si/sv): The ratio of transitional to transversional pairs. This ratio helps in understanding the predominance of mutation types in DNA and can indicate evolutionary pressures or repair mechanisms.
Polymorphic Sites
Genera
Total sites
Conserved sites
Variable sites
Parsim-Info sites
Singleton sites
CpG
Flavivirus
46593
5266
29636
19292
7575
22
Hepacivirus
19168
1834
14408
11964
1861
20
Orthoflavivirus
13627
2225
10437
10330
103
230
Pegivirus
17209
1736
13920
12053
1585
50
Pestivirus
20726
4996
14176
12077
1233
40
1. Conserved Sites: DNA sequence positions that remain unchanged across different individuals or species, indicating evolutionary importance and functional significance.
2. Variable Site: Positions in DNA sequences where variations are observed when comparing different individuals or species, used to study genetic diversity.
3. Parsim-Info Sites: Sites that provide information for the least number of evolutionary changes, useful in phylogenetic construction for simplifying evolutionary assumptions.
4. Singleton Sites: Positions in a DNA sequence that show a mutation in only one individual within a population, potentially indicating recent mutation events.
5. CpG Sites: Specific DNA regions where a cytosine is followed by a guanine, often involved in gene regulation through methylation processes.
Genetic Distance
Genera
Flavivirus
Hepacivirus
Orthoflavivirus
Pegivirus
Pestivirus
Flavivirus
0.7758
0.9526
0.6286
1.1361
0.9541
Hepacivirus
0.9526
0.2841
0.8042
0.5843
0.8395
Orthoflavivirus
0.6286
0.8042
0.3836
1.0393
0.7629
Pegivirus
1.1361
0.5843
1.0393
0.4671
1.0276
Pestivirus
0.9541
0.8395
0.7629
1.0276
0.3427
Pair Frequencies
Serotypes
ii(Identical Pairs)
si(Transitionsal Pairs)
sv(Transversional Pairs)
R(si/sv)
DENV-1
9940
532
115
1.32
DENV-2
9880
632
90
1.43
DENV-3
10150
406
58
1.48
DENV-4
9991
512
83
1.41
DENV
8194
1207
1160
1.01
1. ii (Identical Pairs): Base pairs in DNA that are the same when two sequences are compared. They indicate the degree of similarity or genetic relationship between the sequences.
2. si (Transitional Pairs): Substitutions between purines (A and G) or between pyrimidines (C and T) in DNA. These mutations are more common because of the chemical structure similarities between purines and between pyrimidines.
3. sv (Transversional Pairs): Substitutions between a purine and a pyrimidine (e.g., A to C or T, G to C or T) in DNA. These are less common due to the more significant chemical structure changes involved.
4. R (si/sv): The ratio of transitional to transversional pairs. This ratio helps in understanding the predominance of mutation types in DNA and can indicate evolutionary pressures or repair mechanisms.
Polymorphic Sites
Serotypes
Total sites
Conserved sites
Variable sites
Parsim-Info sites
Singleton sites
CpG
DENV-1
12714
4678
6673
5461
1187
456
DENV-2
11768
4091
7213
5602
1505
302
DENV-3
11065
4907
5985
4830
1114
632
DENV-4
10961
5860
4943
4202
713
816
DENV
13874
2561
9366
7630
1598
112
1. Conserved Sites: DNA sequence positions that remain unchanged across different individuals or species, indicating evolutionary importance and functional significance.
2. Variable Site: Positions in DNA sequences where variations are observed when comparing different individuals or species, used to study genetic diversity.
3. Parsim-Info Sites: Sites that provide information for the least number of evolutionary changes, useful in phylogenetic construction for simplifying evolutionary assumptions.
4. Singleton Sites: Positions in a DNA sequence that show a mutation in only one individual within a population, potentially indicating recent mutation events.
5. CpG Sites: Specific DNA regions where a cytosine is followed by a guanine, often involved in gene regulation through methylation processes.
Genetic Distance
Serotypes
DENV-1
DENV-2
DENV-3
DENV-4
DENV-1
0.0607
0.3557
0.3096
0.3821
DENV-2
0.3557
0.0632
0.3454
0.3765
DENV-3
0.3096
0.3454
0.0423
0.3786
Pegivirus
0.3821
0.3765
0.3786
0.0552