Pythium iwayamai vs Pythium irregulare Translated Blat results

Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) and Pythium irregulare (Pythium irregulare DAOM BR486, pir_scaffolds_v1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 75. Pythium iwayamai 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

ParameterPythium iwayamaiPythium irregulare
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 100,198 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium iwayamai

Uncovered: 24,008,283 out of 43,199,174
Covered: 19,190,891 out of 43,199,174

Uncovered: 4,070,768 out of 19,552,457
Matches: 12,607,845 out of 19,552,457
Mismatches: 2,852,637 out of 19,552,457
Insertions: 21,207 out of 19,552,457
Identity over aligned base-pairs: 81.4%

Pythium irregulare

Uncovered: 25,378,458 out of 42,968,084
Covered: 17,589,626 out of 42,968,084

Uncovered: 5,819,625 out of 20,543,058
Matches: 12,054,587 out of 20,543,058
Mismatches: 2,637,119 out of 20,543,058
Insertions: 31,727 out of 20,543,058
Identity over aligned base-pairs: 81.9%