Pythium arrhenomanes vs Phaeodactylum tricornutum Translated Blat results

Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_scaffolds_v1) and Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 75. Pythium arrhenomanes 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 arrhenomanesPhaeodactylum tricornutum
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 6,959 alignment blocks

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

Uncovered: 43,664,675 out of 44,672,625
Covered: 1,007,950 out of 44,672,625

Uncovered: 17,449,755 out of 18,367,184
Matches: 604,152 out of 18,367,184
Mismatches: 313,115 out of 18,367,184
Insertions: 162 out of 18,367,184
Identity over aligned base-pairs: 65.9%

Phaeodactylum tricornutum

Uncovered: 26,711,291 out of 27,568,093
Covered: 856,802 out of 27,568,093

Uncovered: 13,591,845 out of 14,407,044
Matches: 537,980 out of 14,407,044
Mismatches: 277,049 out of 14,407,044
Insertions: 170 out of 14,407,044
Identity over aligned base-pairs: 66.0%