Variation in Ensembl Chromosome ID

Question

[Mel]

Hi, I've been parsing through some Ensembl CDS files (using BioPython), and I'm getting some variation in how the chromosome ID is specified. Typically it is specified like this: "chromosome:GRCh38:7:142786213:142786224:1". However, other times it is specified like this: 'chromosome:GRCh38:CHR_HSCHR7_2_CTG6:142847306:142847317:1'. Why is this variation present? What does 'CHR_HSCHR7_2_CTG6' specify exactly? Thanks for any clarification or help.

Answer 1

[JC]

That is a haplotype sequence, check https://www.ensembl.org/Help/Faq?id=291 for more information

[Mel]

Excellent! Thank you JC!