Pythium irregulare vs Phaeodactylum tricornutum Translated Blat results

Pythium irregulare (Pythium irregulare DAOM BR486, pir_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 irregulare 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 irregularePhaeodactylum 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 7,173 alignment blocks

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

Uncovered: 41,908,924 out of 42,968,084
Covered: 1,059,160 out of 42,968,084

Uncovered: 19,537,880 out of 20,543,058
Matches: 659,083 out of 20,543,058
Mismatches: 345,950 out of 20,543,058
Insertions: 145 out of 20,543,058
Identity over aligned base-pairs: 65.6%

Phaeodactylum tricornutum

Uncovered: 26,684,655 out of 27,568,093
Covered: 883,438 out of 27,568,093

Uncovered: 13,566,077 out of 14,407,044
Matches: 551,811 out of 14,407,044
Mismatches: 288,917 out of 14,407,044
Insertions: 239 out of 14,407,044
Identity over aligned base-pairs: 65.6%