Table 1 Equivalent positions and reference (Ref) alleles differing between ARS-UCD1.2 (ARS) and Bovine reference sequence (BRS) relative to ARS-UCD1.2 and indicating whether variant positions belong to the pre-defined haplogroup variant set as defined in cattleTree_whole.txt file of MitotoolPy.

From: Recovery of mitogenomes from whole genome sequences to infer maternal diversity in 1883 modern taurine and indicine cattle

ARS position & Ref. allele

BRS position & Ref. allele

Haplogroup variant in MitoToolPy

Comments

222 C

– (deletion)

No

Deletion at position 222

364 G

363 C

No

 

589 C

– (deletion)

No

Deletion at position 589

2538 A

2536 C

Yes (2536 A)

ARS and HG_variants have same base

3345 G

3343 C

No

 

3387 C

3385 T

No

 

3541 A

3539 G

No

 

4321 C

4319 T

No

 

8190 C

8188 T

Yes (8188 C)

ARS and HG_variants have same base

8712 T

8710 C

No

 

9684 C

9682 G

Yes (9682 C)

ARS and HG_variants have same base

12,167 C

12,165 T

Yes (12,165 C)

ARS and HG_variants have same base

13,312 C

13,310 A

Yes (13,310 C)

ARS and HG_variants have same base

15,637 T

15,635 C

No

 
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