You are here: FoswikiMITOMAP WebTopVariants (18 Feb 2019, MarieLott)

Report date: 6 February 2019 View All Variants

Most Frequent Variants in Mitomap ("Top 40")

Analysis of 47412 GenBank sequences, consisting of 5973 lineage L sequences (12.60%), 10135 lineage M sequences (21.38%), and 31304 lineage N sequences (66.03%).

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Variants present at ≥80% in lineages L, M, or N are in yellow. Variants present at ≥50% are in light blue.
rCRS Position Allele HGVS
Notation
Overall Variant
Count
Overall Variant
Frequency
Variant Frequency
in lineage L *
Variant Frequency
in lineage M *
Variant Frequency
in lineage N
*
Ancestral
SNP **
A 15326 G m.15326A>G 46786 98.68% 99.56% 99.09% 98.36% Yes
A 8860 G m.8860A>G 46766 98.64% 99.20% 98.91% 98.44% Yes
A 750 G m.750A>G 46564 98.21% 95.09% 99.69% 98.33% Yes
A 4769 G m.4769A>G 46309 97.67% 99.15% 99.44% 96.82% Yes
A 263 G m.263A>G 45105 95.13% 83.83% 98.02% 96.36% Yes
A 1438 G m.1438A>G 45044 95.01% 83.59% 96.08% 96.83% Yes
C 7028 T m.7028C>T 38351 80.89% 99.77% 99.65% 71.21% Yes
A 2706 G m.2706A>G 37523 79.14% 92.03% 96.81% 70.69% Yes
G 11719 A m.11719G>A 36775 77.56% 99.73% 99.62% 66.20% Yes
C 14766 T m.14766C>T 36489 76.96% 99.78% 95.74% 66.53% Yes
A 73 G m.73A>G 36030 75.99% 85.12% 98.64% 66.92% Yes
A 10398 G m.10398A>G 21096 44.50% 95.16% 99.49% 17.02% Yes
C 12705 T m.12705C>T 19971 42.12% 99.58% 99.35% 12.63% Yes
C 16223 T m.16223C>T 19008 40.09% 92.45% 94.89% 12.36% Yes
A 8701 G m.8701A>G 16079 33.91% 99.36% 99.01% 0.35% Yes
T 9540 C m.9540T>C 16072 33.90% 99.73% 99.54% 0.09% Yes
T 10873 C m.10873T>C 16066 33.89% 99.67% 99.48% 0.10% Yes
G 15301 A m.15301G>A 15805 29.12% 59.74% 99.33% 0.54% No
T 489 C m.489T>C 12223 25.78% 0.07% 98.32% 7.20% No
G 15043 A m.15043G>A 11201 23.62% 1.72% 99.27% 3.31% No
C 10400 T m.10400C>T 10104 21.31% 0.08% 99.59% 0.02% No
T 14783 C m.14783T>C 10078 21.26% 0.00% 99.11% 0.11% No
 

Additional variants present at ≥50% in lineages L, M, or N (in light blue), or in ≥10,000 sequences overall (in light beige)
rCRS Position Allele HGVS
Notation
Overall Variant
Count
Overall Variant
Frequency
Variant Frequency
in lineage L *
Variant Frequency
in lineage M *
Variant Frequency
in lineage N
*
Ancestral
SNP **
T 16519 C m.16519T>C 29838 62.93% 63.54% 55.98% 65.07% Yes **
T 310 C m.310T>C 19485 41.10% 34.91% 41.49% 42.15% No
C 315 CC m.315C>CC 14322 30.21% 38.14% 27.74% 29.49% No
T 152 C m.152T>C 12651 26.68% 63.62% 21.13% 21.43% Yes
C 309 CCT m.309_310insCT 12642 26.66% 16.69% 30.53% 27.32% No
T 16189 C m.16189T>C 12173 25.67% 52.34% 15.48% 23.89% Yes
CA 514_515 d m.514_515delCA 11538 24.34% 51.36% 24.27% 19.20% (Yes) **
T 16311 C m.16311T>C 9335 19.69% 52.25% 15.86% 14.72% Yes
T 195 C m.195T>C 9294 19.60% 55.50% 15.23% 14.17% Yes
C 16278 T m.16278C>T 5010 10.57% 50.95% 6.15% 4.29% Yes
G 7521 A m.7521G>A 3888 8.20% 62.28% 0.43% 0.40% Yes
G 769 A m.769G>A 3882 8.19% 64.41% 0.02% 0.11% Yes
G 1018 A m.1018G>A 3872 8.17% 64.31% 0.11% 0.06% Yes
C 13650 T m.13650C>T 3747 7.90% 62.31% 0.08% 0.05% Yes
C 3594 T m.3594C>T 3740 7.89% 62.43% 0.03% 0.03% Yes
A 4104 G m.4104A>G 3722 7.85% 62.16% 0.00% 0.03% Yes
C 7256 T m.7256C>T 3715 7.84% 61.69% 0.20% 0.03% Yes
A 13105 G m.13105A>G 3604 7.60% 54.33% 1.22% 0.75% Yes

 

* Top Level Haplogroups of Lineages L, M, and N
  • Lineage L ("African"): L0, L1, L2, L3, L4, L5, L6
  • Lineage M ("Asian"): C, D, E, G, M, Q, Z
  • Lineage N ("Eurasian"): A, B, F, H, HV, I, J, K, N, O, P, R, S, T, U, V, W, X, Y

**Ancestral SNPs are common throughout the human mtDNA tree. These ancestral variants, the "RSRS50", are: 73G, 146C, 152C, 195C, 247A, 263G, 750G, 769A, 825A, 1018A, 1438G, 2706G, 2758A, 2885C, 3594T, 4104G, 4312T, 4769G, 7028T, 7146G, 7256T, 7521A, 8468T, 8655T, 8701G, 8860G, 9540C, 10398G, 10664T, 10688A, 10810C, 10873C, 10915C, 11719A, 11914A, 12705T, 13105G, 13276G, 13506T, 13650T, 14766T, 15326G, 16129A, 16187T, 16189C, 16223T, 16230G, 16278T, 16311C, 16519C. Additionally, the RSRS ancestor sequence has two single base deletions, 523d & 524d, located at the end of a string of CA repeats; these are notated by proxy above as 514CA>d. Indels in this region are various and common. Similar length variations are abundant in the region flanked by 308_316. The mutations 309.1C(C), 315.1C, AC indels in region 514_525, and the SNP 16519C are among those specifically excluded by Phylotree in the construction of their master tree.

Topic revision: r12 - 18 Feb 2019, MarieLott

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