Phytophthora lateralis vs Phytophthora infestans Translated Blat results
Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) and Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 76. Phytophthora lateralis was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.
Configuration parameters
Parameter | Value |
---|---|
Minimum score (minScore) | 30 |
Database type (t) | dnax |
Query type (q) | dnax |
Mask out repeats (mask) | lower |
Mask out repeats on query (qMask) | lower |
Chunking parameters
Parameter | Phytophthora lateralis | Phytophthora infestans |
---|---|---|
Chunk size | 1,000,000 | 1,000,000 |
Overlap | 10,000 | 10,000 |
Group set size | 100,000,000 | 100,000,000 |
Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 94,233 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Phytophthora lateralis |
Uncovered: 24,380,680 out of 43,981,379 |
Uncovered: 3,066,773 out of 14,663,433 |
Phytophthora infestans |
Uncovered: 211,033,307 out of 228,543,505 |
Uncovered: 9,298,784 out of 22,421,425 |