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Report date: 23 September 2019

Most Frequent Variants in Mitomap ("Top 40")

There are twelve variants with ≥50% overall frequency that are widespread across all lineages. These are shown in bold.

TABLE 1
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 48493 98.7% 99.6% 99.1% 98.4% Yes
A 8860 G m.8860A>G 48479 98.7% 99.2% 98.9% 98.5% Yes
A 750 G m.750A>G 48276 98.3% 95.1% 99.7% 98.4% Yes
A 4769 G m.4769A>G 48004 97.7% 99.1% 99.4% 96.9% Yes
A 263 G m.263A>G 46799 95.2% 83.9% 98.0% 96.4% Yes
A 1438 G m.1438A>G 46721 95.1% 83.6% 96.1% 96.9% Yes
C 7028 T m.7028C>T 39824 81.1% 99.8% 99.6% 71.3% Yes
A 2706 G m.2706A>G 38981 79.3% 92.1% 96.9% 70.69% Yes
G 11719 A m.11719G>A 38205 77.8% 99.7% 99.6% 66.6% Yes
C 14766 T m.14766C>T 37907 77.1% 99.8% 95.9% 66.9% Yes
A 73 G m.73A>G 37969 76.3% 85.2% 98.7% 67.4% Yes
A 10398 G m.10398A>G 21770 44.3% 95.2% 99.5% 17.1% Yes
C 12705 T m.12705C>T 20517 41.8% 99.6% 99.1% 12.6% Yes
C 16223 T m.16223C>T 19551 39.8% 92.5% 94.8% 12.3% Yes
A 8701 G m.8701A>G 16496 33.6% 99.4% 99.0% 0.3% Yes
T 9540 C m.9540T>C 16490 33.6% 99.7% 99.5% 0.1% Yes
T 10873 C m.10873T>C 16474 33.5% 99.7% 99.3% 0.1% Yes
G 15301 A m.15301G>A 14238 29.0% 59.8% 99.3% 0.5% No
T 489 C m.489T>C 12687 25.8% 0.1% 98.3% 7.1% No
G 15043 A m.15043G>A 11642 23.7% 1.7% 99.3% 3.3% No
C 10400 T m.10400C>T 10506 21.4% 0.1% 99.6% 0.0% No
T 14783 C m.14783T>C 10482 21.3% 0.0% 99.1% 0.1% No
 

TABLE 2
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 30962 63.0% 63.6% 55.6% 65.3% Yes
T 310 C m.310T>C 20139 41.0% 34.8% 41.6% 41.9% No
C 315 CC m.315C>CC 14959 30.4% 38.2% 28.3% 29.7% No
C 309 CCT m.309_310insCT 13100 26.7% 16.7% 30.5% 27.3% No
T 152 C m.152T>C 13034 26.5% 63.7% 21.2% 21.4% Yes
T 16189 C m.16189T>C 12654 25.8% 52.3% 15.5% 24.2% Yes
CA 514_515 d m.514_515delCA 12006 24.4% 51.4% 24.3% 19.2% (Yes)
T 16311 C m.16311T>C 9611 19.6% 52.3% 15.8% 14.7% Yes
T 195 C m.195T>C 9537 19.4% 55.5% 15.2% 14.1% Yes
C 16278 T m.16278C>T 5119 10.4% 51.0% 6.3% 4.3% Yes
G 7521 A m.7521G>A 3918 8.0% 62.3% 0.5% 0.3% Yes
G 769 A m.769G>A 3898 7.9% 64.4% 0.02% 0.1% Yes
G 1018 A m.1018G>A 3884 7.9% 64.3% 0.1% 0.1% Yes
C 13650 T m.13650C>T 3762 7.7% 62.3% 0.1% 0.0% Yes
C 3594 T m.3594C>T 3751 7.6% 62.4% 0.0% 0.0% Yes
A 4104 G m.4104A>G 3733 7.6% 62.1% 0.0% 0.0% Yes
C 7256 T m.7256C>T 3726 7.6% 61.7% 0.2% 0.0% Yes
A 13105 G m.13105A>G 3632 7.4% 54.3% 1.2% 0.8% 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 spread 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. The most widespread across all lineages are shown in bold.

Additionally, the RSRS ancestor sequence has two single base deletions, 523d & 524d, which are located at the end of a string of CA repeats. Indels in this region are variously notated and common. These two deleted bases are not indexed in Mitomap's "RSRS50" set and are among those variants specifically excluded by Phylotree in the construction of their master tree.

Topic revision: r17 - 01 Oct 2019, MarieLott

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