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Report date: 13 September 2018 View All Variants

Most Frequent Variants in Mitomap ("Top 40")

Analysis of 46092 GenBank sequences, consisting of 5891 lineage L sequences (12.78%), 9886 lineage M sequences (21.45%), and 30315 lineage N sequences (65.77%)

Variants present at ≥80% in lineages L, M, or N (in yellow)

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 45479 98.67% 99.56% 99.09% 98.36% Yes
A 8860 G m.8860A>G 45452 98.61% 99.20% 98.89% 98.41% Yes
A 750 G m.750A>G 45251 98.18% 95.03% 99.69% 98.29% Yes
A 4769 G m.4769A>G 45006 97.64% 99.13% 99.42% 96.77% Yes
A 263 G m.263A>G 43811 95.05% 83.91% 98.00% 96.26% Yes
A 1438 G m.1438A>G 43762 94.94% 83.67% 96.04% 96.78% Yes
C 7028 T m.7028C>T 37237 80.79% 99.76% 99.65% 70.95% Yes
A 2706 G m.2706A>G 36421 79.02% 92.12% 96.73% 70.69% Yes
G 11719 A m.11719G>A 35685 77.42% 99.73% 99.61% 65.85% Yes
C 14766 T m.14766C>T 35400 76.80% 99.78% 95.63% 66.20% Yes
A 73 G m.73A>G 34950 75.83% 85.25% 98.60% 66.57% Yes
A 10398 G m.10398A>G 20619 44.73% 95.13% 99.47% 17.09% Yes
C 12705 T m.12705C>T 19540 42.39% 99.58% 99.33% 12.71% Yes
C 16223 T m.16223C>T 18586 40.32% 92.40% 94.87% 12.42% Yes
T 9540 C m.9540T>C 15737 34.14% 99.73% 99.52% 0.08% Yes
T 10873 C m.10873T>C 15733 34.13% 99.66% 99.46% 0.10% Yes
A 8701 G m.8701A>G 15731 34.13% 99.35% 99.00% 0.30% Yes
G 15301 A m.15301G>A 13513 29.32% 59.94% 99.31% 0.54% No
T 489 C m.489T>C 11924 25.87% 0.07% 98.28% 7.27% No
G 15043 A m.15043G>A 10917 23.69% 1.73% 99.25% 3.31% No
C 10400 T m.10400C>T 9855 21.38% 0.08% 99.58% 0.02% No
T 14783 C m.14783T>C 9829 21.32% 0.00% 99.09% 0.11% No
 

Additional variants present at ≥50% in lineages L, M, or N (in light blue), 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 28940 62.79% 63.50% 56.10% 64.83% Yes **
T 310 C m.310T>C 18852 40.90% 35.38% 41.07% 41.92% No
C 315 CC m.315C>CC 13901 30.16% 38.62% 27.70% 29.32% No
T 152 C m.152T>C 12387 26.87% 63.42% 21.35% 21.57% Yes
C 309 CCT m.309_310insCT 12255 26.59% 16.91% 30.14% 27.31% No
T 16189 C m.16189T>C 11745 25.48% 51.96% 15.09% 23.72% Yes
CA 514 d m.513_516del 11165 24.22% 52.03% 24.44% 18.75% (Yes) **
T 16311 C m.16311T>C 9093 19.73% 52.11% 15.67% 14.76% Yes
T 195 C m.195T>C 9078 19.70% 55.44% 15.52% 14.11% Yes
C 16278 T m.16278C>T 4903 10.64% 51.08% 6.18% 4.23% Yes
G 769 A m.769G>A 3815 8.28% 64.17% 0.02% 0.11% Yes
G 7521 A m.7521G>A 3815 8.28% 62.04% 0.45% 0.38% Yes
G 1018 A m.1018G>A 3806 8.26% 64.08% 0.11% 0.07% Yes
C 13650 T m.13650C>T 3681 7.99% 62.08% 0.07% 0.06% Yes
C 3594 T m.3594C>T 3675 7.97% 62.20% 0.03% 0.03% Yes
A 4104 G m.4104A>G 3657 7.93% 61.92% 0.00% 0.03% Yes
C 7256 T m.7256C>T 3650 7.92% 61.45% 0.20% 0.03% Yes
A 13105 G m.13105A>G 3546 7.69% 54.22% 1.24% 0.76% 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: r7 - 13 Sep 2018, MarieLott

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