Table 1.

Summary of genomic analyses.

Sequencing analysis
Number of amplicons attempted	219,229 (100%)
Number of amplicons passing quality control*	208,311 (95%)
Fraction of bases in passing amplicons with PHRED > 20	98.3%
Number of genes analyzed	20,661
Number of transcripts analyzed	23,219
Number of exons analyzed	175,471
Total number of nucleotides successfully sequenced	689,071,123
Number of somatic mutations identified (n = 22 samples)	2,325
Number of somatic mutations (excluding Br27P)	993
Missense	622
Nonsense	43
Insertion	3
Deletion	46
Duplication	7
Splice site or UTR	27
Synonymous	245
Average number of sequence alterations per sample	47.3
Copy number analysis
Total number of SNP loci assessed for copy number changes	1,069,688
Number of copy number alterations identified (n = 22 samples)	281
Amplifications	147
Homozygous deletions	134
Average number of amplifications per sample	6.7
Average number of homozygous deletions per sample	6.1

^*Passing amplicons were defined as having PHRED20 scores or better over 90% of the target sequence in 75% of samples analyzed [see (12) for additional information].