| | FLUORESCENCE-BASED DNA SEQUENCING OF PCR AMPLICONS |
| | DNA sequencing was performed on an ABI 3700 DNA Analyzer. |
| | All base calling for sequence chromatograms was done using Phred. |
| | Polymorphism discovery was performed by alignment of sequencing chromatograms from multiple individuals using Phrap followed by analysis using the PolyPhred computer program to identify single nucleotide polymorphisms. |
| | Program settings for PolyPhred (v. 4.0x) were: |
| | -quality 25 |
| | -window 40 |
| | -rank 3 |
| | -scale1 1.00 |
| | -scale2 1.00 |
| | -tag genotype |
| | -group .+ |
| | Genotypes for individual samples at each polymorphic site were assigned by PolyPhred. |
| | All polymorphic sites and individual genotypes were confirmed by visual inspection. |
| | Multiple strand coverage was available for greater than 40% of scanned sequence, with >99% confirmatio for called genotypes. |
| | PARAMETER: |
| | SEQUENCING_INSTRUMENT: ABI 3700 DNA ANALYZER |
| | BASE_CALLING_PROGRAM: PHRED |
| | ASSEMBLY_PROGRAM: PHRAP |
| | POLYMORPHISM_DETECTION_PROGRAM: POLYPHRED_4.0x |
| | POLYPHRED_QUALITY: 25 |
| | POLYPHRED_SCALE1: 1.0 |
| | POLYPHRED_SCALE2: 1.0 |
| | POLYPHRED_GROUP: .+ |
| | POLYPHRED_RANK: RANK_3 |
| | GENOTYPES_ASSIGNED: POLYPHRED |
| | MULTI_STRAND_COVERAGE: > 0.40 |
