Pythium iwayamai vs Phaeodactylum tricornutum Translated Blat results

Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 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 iwayamaiPhaeodactylum 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 6,634 alignment blocks

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

Uncovered: 42,240,113 out of 43,199,174
Covered: 959,061 out of 43,199,174

Uncovered: 18,670,415 out of 19,552,457
Matches: 580,055 out of 19,552,457
Mismatches: 301,912 out of 19,552,457
Insertions: 75 out of 19,552,457
Identity over aligned base-pairs: 65.8%

Phaeodactylum tricornutum

Uncovered: 26,762,912 out of 27,568,093
Covered: 805,181 out of 27,568,093

Uncovered: 13,644,574 out of 14,407,044
Matches: 501,798 out of 14,407,044
Mismatches: 260,453 out of 14,407,044
Insertions: 219 out of 14,407,044
Identity over aligned base-pairs: 65.8%