Phaeodactylum tricornutum vs Pythium ultimum Translated Blat results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) 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 70. Phaeodactylum tricornutum 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

ParameterPhaeodactylum tricornutumPythium 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 6,821 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phaeodactylum tricornutum

Uncovered: 26,543,060 out of 27,568,093
Covered: 1,025,033 out of 27,568,093

Uncovered: 13,443,278 out of 14,407,044
Matches: 635,242 out of 14,407,044
Mismatches: 328,292 out of 14,407,044
Insertions: 232 out of 14,407,044
Identity over aligned base-pairs: 65.9%

Pythium ultimum

Uncovered: 44,006,317 out of 44,913,582
Covered: 907,265 out of 44,913,582

Uncovered: 18,993,666 out of 19,826,256
Matches: 548,322 out of 19,826,256
Mismatches: 284,133 out of 19,826,256
Insertions: 135 out of 19,826,256
Identity over aligned base-pairs: 65.9%