chromosome name confusion
I have downloaded a GENCODE track from UCSC genome browser which has the list of genes and their genomic positions. However, for some genes, I am confused with the chromosome name. For example, I have seen chr15_KI270905v1_alt as a chromosome. I know there is chromosome 15 but what does chr15_KI270905v1_alt mean?
• 1,071 views
•
link
updated
by
Ram
•
written
by
irfanwustl •
•
written
by
irfanwustl •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Where can I find a complete mapping of Gencode versions to Ensembl versions?
written by Ryan •
-
List of all promoter position
written by irfanwustl •
-
Downloading hg38 centromere and telomere positions from UCSC table browser
written by graeme.thorn
-
Trying to download gencode v29 basic annotation without splice variants
written by geoffcollins7 •
-
retrieve chromosome index
written by niutster
-
Difference between the Fasta files from UCSC and Gencode/Ensembl
written by ATRX
-
nearby gene and miRNA of non coding RNA
written by donny.dw •
-
SNPs and genes IDs from UCSC table browser
written by Aura •
-
Map Genomic Positions Onto Rat Genome
written by Emempe •
-
How Do I Get The Gene Names From The Chromosome Locations In A Wig File
written by pixie@bioinfo
This might be useful: https://gatk.broadinstitute.org/hc/en-us/articles/360041155232-Reference-Genome-Components
_alt"chromosomes" are called alt contigs. These are not really chromosomes; they're contigs (contiguous sequences). The reference genome is made of a bunch of contigs, of which the principal ones are chromosome-wide contigs.