Phytophthora lateralis vs Phaeodactylum tricornutum Translated Blat results

Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) 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 76. Phytophthora lateralis 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

ParameterPhytophthora lateralisPhaeodactylum 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 5,914 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora lateralis

Uncovered: 43,117,461 out of 43,981,379
Covered: 863,918 out of 43,981,379

Uncovered: 13,877,597 out of 14,663,433
Matches: 512,792 out of 14,663,433
Mismatches: 272,944 out of 14,663,433
Insertions: 100 out of 14,663,433
Identity over aligned base-pairs: 65.3%

Phaeodactylum tricornutum

Uncovered: 26,856,888 out of 27,568,093
Covered: 711,205 out of 27,568,093

Uncovered: 13,733,519 out of 14,407,044
Matches: 439,534 out of 14,407,044
Mismatches: 233,792 out of 14,407,044
Insertions: 199 out of 14,407,044
Identity over aligned base-pairs: 65.3%