Pythium irregulare vs Pythium ultimum Translated Blat results

Pythium irregulare (Pythium irregulare DAOM BR486, pir_scaffolds_v1) and Pythium ultimum (Pythium ultimum DAOM BR144, pug) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 75. Pythium irregulare 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 irregularePythium ultimum
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 85,201 alignment blocks

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

Uncovered: 25,970,772 out of 42,968,084
Covered: 16,997,312 out of 42,968,084

Uncovered: 5,987,067 out of 20,543,058
Matches: 11,360,498 out of 20,543,058
Mismatches: 3,175,716 out of 20,543,058
Insertions: 19,777 out of 20,543,058
Identity over aligned base-pairs: 78.0%

Pythium ultimum

Uncovered: 28,973,846 out of 44,913,582
Covered: 15,939,736 out of 44,913,582

Uncovered: 6,495,123 out of 19,826,256
Matches: 10,454,829 out of 19,826,256
Mismatches: 2,863,672 out of 19,826,256
Insertions: 12,632 out of 19,826,256
Identity over aligned base-pairs: 78.4%