Albugo laibachii vs Pythium ultimum Translated Blat results

Albugo laibachii (Albugo laibachii, ENA1) 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 67. Albugo laibachii 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

ParameterAlbugo laibachiiPythium 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 32,352 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Albugo laibachii

Uncovered: 26,884,908 out of 32,766,811
Covered: 5,881,903 out of 32,766,811

Uncovered: 10,794,538 out of 15,902,867
Matches: 3,442,669 out of 15,902,867
Mismatches: 1,664,775 out of 15,902,867
Insertions: 885 out of 15,902,867
Identity over aligned base-pairs: 67.4%

Pythium ultimum

Uncovered: 40,136,265 out of 44,913,582
Covered: 4,777,317 out of 44,913,582

Uncovered: 15,655,164 out of 19,826,256
Matches: 2,811,473 out of 19,826,256
Mismatches: 1,359,013 out of 19,826,256
Insertions: 606 out of 19,826,256
Identity over aligned base-pairs: 67.4%