You'll probably want to be a bit more critical, here. The number of resulting reads is a function of the number of clusters. If the number of clusters is too low, you get a high percentage of reads passing filters, but still a low number of reads. If the number of clusters is too high, you get a low number of reads, but a low percentage of reads passing filters. In our group, the former is the more likely problem; learning how much DNA to load is tricky, it seems. So, look at the number of clusters and compare that to what Illumina says you should be running.

Hello.

At first, I am newbie to NGS, and our data is premitive one.[?] I think we can get about PF-cleared 30 - 35 millions clusters from one lane, when you use GA IIx with Truseq reagents.

This is a plot of cluster density by illumina's SAV (our first result). https://skitch.com/mako/ffcyc/null-status

The lane 2 produced 10145091, 11059614 and 11014741 seqeunces (reported by FastQC).[?] The condition of lane 2 were:

• 3plex with TruSeq reagents and human exome.
• 100 bp Paired-end

I hope this helps you.

Answer I got from our sequencing facility: "You could definitely get more reads out of a GAIIx run: typical post-filter read counts are 30 million reads or better, topping out a little less than 40 million."