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Report date: 2020-06-26
View All FL Sequence Variants
FL Sequence Variants satisfying ClinGen BA1-BS1

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 50503 98.7% 99.6% 99.1% 98.3% Yes
A 8860 G m.8860A>G 50409 98.5% 99.0% 98.9% 98.2% Yes
A 750 G m.750A>G 50304 98.3% 95.3% 99.7% 98.4% Yes
A 4769 G m.4769A>G 49949 97.6% 99.0% 99.4% 96.7% Yes
A 263 G m.263A>G 48560 94.9% 81.7% 98.0% 96.2% Yes
A 1438 G m.1438A>G 48542 94.8% 81.5% 96.1% 96.8% Yes
C 7028 T m.7028C>T 41344 80.8% 99.8% 99.6% 71.3% Yes
A 2706 G m.2706A>G 40409 78.9% 90.8% 96.9% 71.0% Yes
G 11719 A m.11719G>A 39624 77.4% 99.7% 99.6% 66.3% Yes
C 14766 T m.14766C>T 39357 76.9% 99.8% 95.9% 66.6% Yes
A 73 G m.73A>G 38860 75.9% 85.2% 98.6% 67.0% Yes
A10398Gm.10398A>G2256544.1%95.3%99.5%17.1%Yes
C12705Tm.12705C>T2120841.4%99.5%99.1%12.4%Yes
C16223Tm.16223C>T2016939.4%92.0%94.7%12.2%Yes
A8701Gm.8701A>G1705033.3%99.4%99.0%0.3%Yes
T9540Cm.9540T>C1704433.3%99.7%99.5%0.1%Yes
T10873Cm.10873T>C1703333.3%99.6%99.3%0.1%Yes
G15301Am.15301G>A1459828.5%57.9%99.3%0.6%No
T489Cm.489T>C1314625.7%0.1%98.3%7.2%No
G15043Am.15043G>A1201923.5%1.7%99.3%3.3%No
C10400Tm.10400C>T1084021.2%0.1%99.5%0.0%No
T14783Cm.14783T>C1081621.1%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 32160 62.8% 64.5% 55.6% 64.8% Yes
T310Cm.310T>C2069540.4%33.7%41.4%41.4%No
C315CCm.315_316insC1562030.5%37.2%28.4%30.0%No
T152Cm.152T>C1347326.3%63.2%20.8%21.4%Yes
C309CCTm.309_310insCT1338426.1%16.1%30.1%26.7%No
T16189Cm.16189T>C1310625.6%53.6%15.3%23.8%Yes
CA514dm.514_515delCA1220323.8%49.7%24.3%19.0%†††
T16311Cm.16311T>C1016019.8%53.9%16.4%14.7%Yes
T195Cm.195T>C998619.5%56.3%15.2%14.2%Yes
C16278Tm.16278C>T523910.2%50.1%6.1%4.3%Yes
G7521Am.7521G>A41318.1%63.4%0.5%0.4%Yes
G769Am.769G>A41178.0%65.6%0.0%0.1%Yes
G1018Am.1018G>A40988.0%65.5%0.1%0.1%Yes
C13650Tm.13650C>T39707.8%63.5%0.1%0.1%Yes
C3594Tm.3594C>T39597.7%63.6%0.0%0.0%Yes
A4104Gm.4104A>G39427.7%63.3%0.0%0.0%Yes
C7256Tm.7256C>T39357.7%62.9%0.2%0.0%Yes
A13105Gm.13105A>G38597.5%55.7%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. The beginning of this particular CA repeat string is at position 514; an alternate call of “514_515d” for this 523_524d deletion is often used. 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: r18 - 29 Jun 2020, UnknownUser

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