Phaeodactylum tricornutum vs Albugo laibachii Translated Blat results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) and Albugo laibachii (Albugo laibachii, ENA1) 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 tricornutumAlbugo laibachii
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 5,650 alignment blocks

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

Uncovered: 26,694,796 out of 27,568,093
Covered: 873,297 out of 27,568,093

Uncovered: 13,586,798 out of 14,407,044
Matches: 533,217 out of 14,407,044
Mismatches: 286,870 out of 14,407,044
Insertions: 159 out of 14,407,044
Identity over aligned base-pairs: 65.0%

Albugo laibachii

Uncovered: 32,004,704 out of 32,766,811
Covered: 762,107 out of 32,766,811

Uncovered: 15,175,318 out of 15,902,867
Matches: 472,018 out of 15,902,867
Mismatches: 255,371 out of 15,902,867
Insertions: 160 out of 15,902,867
Identity over aligned base-pairs: 64.9%