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

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* 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.