liftover from hg19 to hg38 of 1000 G phase 1 data charomosomes

353 views

Skip to first unread message

Aniket Mishra

unread,

Nov 13, 2014, 11:48:54 AM11/13/14

to gen...@soe.ucsc.edu

Dear Sir/Ma’m,

I ran liftover to convert 1000 Genomes phase 1 data from hg19 to hg38. For around 1855 SNPs I got following chromosomes. Could you please explain what is this?

11_KI270927v1_alt, 12_GL877875v1_alt, 14_GL000009v2_random, 14_KI270726v1_random, 14_KI270846v1_alt, 15_KI270850v1_alt, 17_KI270857v1_alt, 17_KI270860v1_alt, 17_KI270862v1_alt, 17_KI270909v1_alt, 19_KI270938v1_alt, 1_KI270706v1_random, 1_KI270765v1_alt, 1_KI270766v1_alt, 22_KI270879v1_alt, 22_KI270928v1_alt, 2_GL383522v1_alt, 2_KI270773v1_alt, 2_KI270776v1_alt, 2_KI270894v1_alt, 4_GL000008v2_random, 7_KI270803v1_alt, 8_KI270821v1_alt, Un_KI270742v1

Thanks

Aniket

Aniket Mishra

PhD Research Student

Statistical Genetics Group

Queensland Institute of Medical Research

300 Herston Road

Brisbane QLD 4029, Australia

Mailing Address:

Queensland Institute of Medical Research

Locked Bag 2000, Herston, QLD 4029, Australia

Tel. +61 7 3362 0809

Aniket...@qimr.edu.au

Matthew Speir

unread,

Nov 13, 2014, 7:11:38 PM11/13/14

to Aniket Mishra, gen...@soe.ucsc.edu

Hi Aniket,

Thank you for your question about chromosome naming conventions for the GRCh38/hg38 human assembly. Please see the "Chromosome naming conventions" section of the hg38 gateway page, http://genome.ucsc.edu/cgi-bin/hgGateway?&db=hg38, for an explanation of what these "alt" and "random" chromosomes represent.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group