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A new paper, just published yesterday:
http://biorxiv.org/content/early/2017/03/03/113241
http://biorxiv.org/content/biorxiv/e...13241.full.pdf
http://biorxiv.org/content/biorxiv/s...1/113241-1.pdf
Supplementary Information Section 3
Y chromosomal haplogroup analysis
We were able to determine the Y chromosomal haplogroup by examining a set of
diagnostic positions on chromosome Y using the ISOGG database (http://isogg.org/,
accessed in 2016 March). In order to perform this analysis, we restricted our analysis
to only include reads with a mapping quality higher than 30. Afterwards, we
determined the haplogroups by identifying the most derived Y chromosomal SNP in
our individual.
Spiginas1 could be assigned as I2a1a2a1a based on L233:G→A (2x). This individual
also has one upstream mutations for haplogroup I2a1a2a (L1286: G→A at 1x) and
one mutation for I2a1 (PF4004: T→C at 1x) and I2a (L460: A→C at 1x).
Kretuonas2 has a derived allele at I2a1b1:C→T, however only with coverage of 1x.
Due to missing significance at that position we are not confident in this assignment.
We were however able to find multiple upstream mutations assigning this individual
to I2a1b (CTS176, CTS1293, CTS1802, CTS5375, CTS7218, and S2702). We are
confident that the placement of this sample in Y chromosomal haplogroup I2a1b is
correct.
Gyvakarai1 could be assigned as R1a1a1b based on S441:G→A (6x) and
S224:C→T (3x). This individual also has two upstream mutations for haplogroup
R1a1a1 (M417 and Page7) and multiple mutations for R1a1a (M515, M198, L168,
M512, and L449) and R1a1 (PF6234, M459, and M448). We are confident that the
placement of this sample in Y chromosomal haplogroup R1a1a1b is correct.
Kunila2 has a derived allele at R1a1a1b:C→T, however only with coverage of 1x.
Due to missing significance at that position we are not confident in this assignment.
We were able to find one upstream mutation assigning this individual to R1a1a1
(Page7: C→T at 1x), two mutations assigning this individual to R1a1a (M198:C→T
at 2x and M512:C→T at 1x) and one mutation to R1a1 (PF6234: C→T at 1x).
Spiginas2 could be assigned as R1a1a1b based on S441:G→A (3x). This individual
also has multiple upstream mutations for haplogroup R1a1a (M515, L168, M512,
M514, L449), R1a1 (PF6234 and L120) and R1a (L63 and L146).
Olsund could be assigned as R1a1a1b based on S441:G→A (3x). This individual
also has multiple upstream mutations for haplogroup R1a1a (M515, L168 and L449),
R1a1 (M459) and R1a (L63 and PF6175).
Turlojiske3 could be assigned as R1a1a1b based on S441:G→A (1x). This individual
also has one upstream mutation for haplogroup R1a1a (L168:A→G at 1x), R1a1
(PF6234:C→T at 2x) and R1a (L62 and L63).
Kivutkalns19 could be assigned as R1a1a1b based on S441:G→A (4x) and
S224:C→T (1x). This individual also has two upstream mutations for haplogroup
R1a1a1 (M417 and Page7) and two mutations for R1a1a (M515 and L449) and R1a1
(PF6234 and M459). We are confident that the placement of this sample in Y
chromosomal haplogroup R1a1a1b is correct.
Kivutkalns25 could be assigned as R1a1a1b based on S441:G→A (3x). This
individual also has one upstream mutation for haplogroup R1a1a1 (M417) and two
mutations for R1a1a (M515 and L449) and R1a1 (M516 and M459). We are
confident that the placement of this sample in Y chromosomal haplogroup R1a1a1b is
correct.
Kivutkalns194 has a derived allele at R1a1a-L168:A→G. We were able to find one
upstream mutation assigning this individual to R1a (L62:A→G at 2x) and one
mutation assigning this individual to R1 (P286: C→T at 2x).
Kivutkalns209 has a derived allele at R1a1a1-Page7:C→T, however only with
coverage of 1x. Therefore we are not convinced that this represents the truth assigning
this individual to R1a1a1, due to missing significance at that position. We were
however able to find two upstream mutation assigning this individual to R1a1a
(M515: T→A at 1x, L168:A→G at 4x) and multiple mutations assigning this
individual to R1a1 (PF6234, L120 and M459). We are confident that the placement of
this sample in Y chromosomal haplogroup R1a1a is correct.
Kivutkalns222 has a derived allele at R1a1a1-M417:G→A, however only with
coverage of 1x. Therefore we are not convinced that this represents the truth assigning
this individual to R1a1a1, due to missing significance at that position. We were able
to find one upstream mutation assigning this individual to R1a1a (M512: C→T at 1x),
one mutation assigning this individual to R1a1 (M459:A→G at 1x) and one mutation
to R1a (L62: A→G at 4x) and are confident with an assignment to R1a1.
Due to low coverage no assignment could be made for Popovo2.
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