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Report date: 04/02/18 View All Variants

Most Frequent Variants in Mitomap ("Top 40")

Analysis of 42,616 GenBank sequences, consisting of 5256 lineage L sequences (12.33%), 9110 lineage M sequences (21.38%), and 28250 lineage N sequences (66.29%)

Variants present at ≥80% in lineages L, M, or N:

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 8860 G m.8860A>G 42037 98.64% 99.16% 99.12% 98.39% Yes
A 15326 G m.15326A>G 42014 98.59% 99.52% 99.08% 98.25% Yes
A 750 G m.750A>G 41819 98.13% 95.05% 99.68% 98.20% Yes
A 4769 G m.4769A>G 41631 97.69% 99.05% 99.56% 96.83% Yes
A 1438 G m.1438A>G 40444 94.90% 83.54% 95.75% 96.74% Yes
A 263 G m.263A>G 40440 94.89% 83.69% 97.88% 96.01% Yes
C 7028 T m.7028C>T 34322 80.54% 99.73% 99.66% 70.80% Yes
A 2706 G m.2706A>G 33566 78.76% 92.43% 96.48% 70.51% Yes
G 11719 A m.11719G>A 32908 77.22% 99.70% 99.59% 65.82% Yes
C 14766 T m.14766C>T 32666 76.65% 99.75% 95.80% 66.18% Yes
A 73 G m.73A>G 32275 75.73% 85.77% 98.51% 66.52% Yes
A 10398 G m.10398A>G 18887 44.32% 95.15% 99.43% 17.09% Yes
C 12705 T m.12705C>T 17860 41.91% 99.54% 99.29% 12.68% Yes
C 16223 T m.16223C>T 16947 39.77% 92.09% 94.71% 12.32% Yes
T 9540 C m.9540T>C 14325 33.61% 99.71% 99.50% 0.07% Yes
T 10873 C m.10873T>C 14317 33.60% 99.62% 99.43% 0.08% Yes
A 8701 G m.8701A>G 14313 33.59% 99.30% 98.97% 0.28% Yes
G 15301 A m.15301G>A 12380 29.05% 60.67% 99.26% 0.52% No
T 489 C m.489T>C 11111 26.07% 0.08% 99.18% 7.33% No
G 15043 A m.15043G>A 9992 23.45% 0.93% 99.19% 3.21% No
C 10400 T m.10400C>T 9078 21.30% 0.10% 99.54% 0.02% No
T 14783 C m.14783T>C 9052 21.24% 0.00% 99.01% 0.11% No

Variants present at ≥50% in lineages L, M, or N, or in ≥10,0000 sequences overall:

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 26796 62.88% 63.47% 56.48% 64.83% Yes **
T 310 C m.310T>C 17998 42.23% 42.23% 36.32% 43.78% No
C 315 CC m.315C>CC 13012 30.53% 39.40% 28.89% 29.41% No
C 309 CCT m.309_310insCT 11665 27.37% 15.96% 32.16% 27.95% No
T 152 C m.152T>C 11342 26.61% 63.68% 21.08% 21.50% Yes
T 16189 C m.16189T>C 10744 25.21% 52.32% 14.53% 23.61% Yes
CA 514 d m.513_516del 10416 24.44% 50.86% 25.19% 19.28% (Yes) **
T 195 C m.195T>C 8308 19.50% 56.22% 15.47% 13.96% Yes
T 16311 C m.16311T>C 8247 19.35% 50.00% 16.08% 14.70% Yes
C 16278 T m.16278C>T 4502 10.56% 52.34% 5.93% 4.29% Yes
G 7521 A m.7521G>A 3447 8.09% 62.80% 0.41% 0.39% Yes
G 769 A m.769G>A 3428 8.04% 64.67% 0.02% 0.10% Yes
G 1018 A m.1018G>A 3428 8.04% 64.63% 0.12% 0.07% Yes
C 13650 T m.13650C>T 3327 7.81% 62.84% 0.08% 0.06% Yes
C 3594 T m.3594C>T 3320 7.79% 62.99% 0.03% 0.02% Yes
A 4104 G m.4104A>G 3299 7.74% 62.67% 0.00% 0.02% Yes
C 7256 T m.7256C>T 3292 7.72% 62.14% 0.19% 0.03% Yes
A 13105 G m.13105A>G 3148 7.39% 53.67% 1.15% 0.79% 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: r4 - 02 Apr 2018, MarieLott
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