coordinate does not match sequence between IGB and IGV

Question

[solo7773]

As shown in igv, base at position 2112413 from hg19 is T

but in igb base at position 2112413 from hg19 is C

however in igb base at position 2112412 is T, the same as position 2112413 in igv

Can any body tell me which is right?

Thanks a lot

• Nan

[Denise CS]

I've checked this in Ensembl and UCSC. Both show G (or C) at 1:2112412 (GRCh37=hg19). It seems the sources of the Hosted Genomes in IGV is UCSC, so I'd expect them to agree. Can you contact IGV and see what they say?

[solo7773]

Thanks Denise. I contacted IGB developer. They told me the difference comes from different numbering methods used between IGB (interbase coordinates) and IGV (one-base coordinates). In inter base, the bases numbered from 0 but in one-base numbered from 1 (refer to http://transvar.org/6111/interbase.pdf for more info), resulting in the difference as we've seen. Of note, one-base method is popular and widely used in bioinformatics programs. That is why coordinates among IGV, Ensembl and UCSC are the same.

[Denise CS]

One-base method is indeed used by Ensembl (What human genome assembly and coordinate system is Ensembl using?) but it seems UCSC has got a combination of both depending on how you enter your coordinates (position format versus BED) (Database/browser start coordinates differ by 1 base).

[solo7773]

Thanks Denise, for the details you gave. Even though UCSC gives different results for position format and BED format. Actually, the core internal database presentation is still zero-based start and one-based end. As database is the data where the data from, I think either position format or BED format is just a presentation of the internal zero-based database. But, this can easily make people confused, as the help webpage says.

Answer 1

[solo7773]

Do the add comment and add your answer function differently in biostar?