Phytophthora kernoviae vs Phytophthora infestans Translated Blat results
Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) 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 kernoviae 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 kernoviae | 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 74,795 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Phytophthora kernoviae |
Uncovered: 25,223,096 out of 43,208,681 |
Uncovered: 2,447,178 out of 11,508,642 |
Phytophthora infestans |
Uncovered: 211,732,124 out of 228,543,505 |
Uncovered: 7,898,682 out of 22,421,425 |