What Is The Refseq Id For Illumina Phix Control?

Question

[Tawny]

I think I know what the gene identifier for the Illumina PhiX control is. I have GI:9626372 RefSeq:NC_001422.

Can any one confirm that those identifiers are what Illumina uses for the PhiX control?

Thank you.

Answer 1

[Zev.Kronenberg]

Illumina uses NC_001422

http://www.ncbi.nlm.nih.gov/nucleotide/NC_001422

This question has already been answered:

http://seqanswers.com/forums/showthread.php?p=38679

[Tawny]

Thanks for the link. My question is: Are the identifying numbers listed above the same sequence/organism that is used by Illumina?

[Zev.Kronenberg]

see changes above.

Answer 2

[igor]

There are actually some minor differences between the Illumina and NCBI PhiX sequences. From the iGenomes README file:

Feb 2, 2011

There are 5 single-nucleotide differences between the PhiX sequence from NCBI and the PhiX sequence from Illumina. Both sequences have length of 5386 bp. The difference are (in 1-based coordinates):

Position    NCBI    Illumina
----------------------------
587         G       A
833         G       A
2731        A       G
2793        C       T
2811        C       T

The Illumina Phix sequence is used by RTA to report initial error rates. Note that in practice some sites in PhiX are heterozygous.