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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

ParameterValue
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

ParameterPhytophthora kernoviaePhytophthora infestans
Chunk size1,000,0001,000,000
Overlap10,00010,000
Group set size100,000,000100,000,000
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
Covered: 17,985,585 out of 43,208,681

Uncovered: 2,447,178 out of 11,508,642
Matches: 7,000,753 out of 11,508,642
Mismatches: 2,047,036 out of 11,508,642
Insertions: 13,675 out of 11,508,642
Identity over aligned base-pairs: 77.3%

Phytophthora infestans

Uncovered: 211,732,124 out of 228,543,505
Covered: 16,811,381 out of 228,543,505

Uncovered: 7,898,682 out of 22,421,425
Matches: 10,987,498 out of 22,421,425
Mismatches: 3,523,609 out of 22,421,425
Insertions: 11,636 out of 22,421,425
Identity over aligned base-pairs: 75.7%