Pythium irregulare vs Pythium aphanidermatum Translated Blat Results

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Pythium irregulare (Pythium irregulare DAOM BR486, pir_scaffolds_v1) and Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Pythium irregulare was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 59,798

Genome coverage (bp) Coding exon coverage (bp)
Pythium irregulare DAOM BR486

Uncovered: 31,986,506 out of 42,968,084
Covered: 10,981,578 out of 42,968,084

Uncovered: 10,659,661 out of 20,543,058
Matches: 7,164,999 out of 20,543,058
Mismatches: 2,713,208 out of 20,543,058
Insertions: 5,190 out of 20,543,058

Pythium aphanidermatum DAOM BR444

Uncovered: 25,858,494 out of 35,876,849
Covered: 10,018,355 out of 35,876,849

Uncovered: 9,185,962 out of 18,015,574
Matches: 6,434,769 out of 18,015,574
Mismatches: 2,391,040 out of 18,015,574
Insertions: 3,803 out of 18,015,574

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

Pythium irregulare Pythium aphanidermatum
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}