Angela
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I posted this on another thread, but I think it should probably also be posted in the ancient dna section in case it gets buried.
In the supplement to this paper we can find this:
"We also evaluated SNPs in our reconstructed human mitochondrial genomes. All SNPs were called by Geneious (v. 7.1.2) (http://www.geneious.com)[S41] at 5X coverage and 90% minimum variant frequency and also interpreted via HaploGrep2 [S53], with mutations indicated(absent, expected, private). The haplogroup of each individual was determined using HaploGrep2 [S53] from a consensus fasta file generated from the mitochondrial alignments, with the resultant SNP calls compared between HaploGrep2 [S53] and PhyloTree Build 17 [S54]: the haplogroup for sample LG20 is consistent with T2c1e (88.16% quality score) and LV13 is consistent with haplogroup T2b29 (62.17% quality score). "
This is the link to the paper:
http://www.cell.com/current-biology/...822(16)31201-5
This is the link to the supplement:
http://www.cell.com/cms/attachment/2...98569/mmc1.pdf
The mtDna T2c1e (LG20) comes from Vagnari.
The mtDna T2b29 (LV13) comes from Velia.
In the supplement to this paper we can find this:
"We also evaluated SNPs in our reconstructed human mitochondrial genomes. All SNPs were called by Geneious (v. 7.1.2) (http://www.geneious.com)[S41] at 5X coverage and 90% minimum variant frequency and also interpreted via HaploGrep2 [S53], with mutations indicated(absent, expected, private). The haplogroup of each individual was determined using HaploGrep2 [S53] from a consensus fasta file generated from the mitochondrial alignments, with the resultant SNP calls compared between HaploGrep2 [S53] and PhyloTree Build 17 [S54]: the haplogroup for sample LG20 is consistent with T2c1e (88.16% quality score) and LV13 is consistent with haplogroup T2b29 (62.17% quality score). "
This is the link to the paper:
http://www.cell.com/current-biology/...822(16)31201-5
This is the link to the supplement:
http://www.cell.com/cms/attachment/2...98569/mmc1.pdf
The mtDna T2c1e (LG20) comes from Vagnari.
The mtDna T2b29 (LV13) comes from Velia.
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