Hi All,
I had a metagenomic run on MiSeq using v3 kits of 16s rRNA v3-v4 region. I have loaded 8pM pooled library with 10% PhiX spike-in. MiSeq run had 89% PF with 16 M raw reads but with very low q30 37.5%. I am surprised how come q30 score that too much low even having good PF of 89%.
I also see a large variation in % reads representation for a few samples (21-samples) out of 257 samples. Could this result in low Q30 of MiSeq run, but how ?
I am attaching a few SAV screenshots for reference.
Thanks
I had a metagenomic run on MiSeq using v3 kits of 16s rRNA v3-v4 region. I have loaded 8pM pooled library with 10% PhiX spike-in. MiSeq run had 89% PF with 16 M raw reads but with very low q30 37.5%. I am surprised how come q30 score that too much low even having good PF of 89%.
I also see a large variation in % reads representation for a few samples (21-samples) out of 257 samples. Could this result in low Q30 of MiSeq run, but how ?
I am attaching a few SAV screenshots for reference.
Thanks
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