I recently got back a lot of sequencing data from an Illumina MiSeq run with very low genetic variation. I want to make sure that the low genetic variation is a result of natural genetic variation instead of sequencing error. I emailed my sequencing facility and no on has responded. I know that PhiX is commonly used as a quality control to test sequencing error rates.
Does anyone know the sequencing error rate with PhiX on a Illumina MiSeq (NOT HiSeq)??
Thanks!
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anin.gregory
I recently got back a lot of sequencing data from an Illumina MiSeq run with very low genetic variation.
What do you mean by that ? you mean low complexity ? Low genetic variation (to me) can mean either:
I want to make sure that the low genetic variation is a result of natural genetic variation instead of sequencing error.
still confused.
I emailed my sequencing facility and no on has responded. I know that PhiX is commonly used as a quality control to test sequencing error rates. Does anyone know the sequencing error rate with PhiX on a Illumina MiSeq (NOT HiSeq)??
Are you looking at the RTA report ? For a 76bp run, we get errors under 0.5%, for 125bp, we cross the 1% error rate after 100bp, for 200bp we get easily 4-5% at the ends.
we were given fully assembled genomes back from our sequencing facility and they did not give us an RTA report.
By low genetic variation I am mean that there are very few heterozygous sites.
ok, maybe I am slow today but could you explain the conceptual correlation between the low # of het. sites and phiX error because I fail to see it.
another comment, do not rely on biostars to get your PhiX error rate. Either get the RTA report or align the controls back to the PhiX and plot your error rate. Even aligning gives you underestimated error rates.
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