Giardia lamblia vs Albugo laibachii Translated Blat results

Giardia lamblia (Giardia lamblia, GL2) 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. Giardia lamblia 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

ParameterGiardia lambliaAlbugo 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 1,040 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Giardia lamblia

Uncovered: 11,039,839 out of 11,192,215
Covered: 152,376 out of 11,192,215

Uncovered: 9,172,564 out of 9,322,001
Matches: 93,896 out of 9,322,001
Mismatches: 55,523 out of 9,322,001
Insertions: 18 out of 9,322,001
Identity over aligned base-pairs: 62.8%

Albugo laibachii

Uncovered: 32,631,191 out of 32,766,811
Covered: 135,620 out of 32,766,811

Uncovered: 15,772,122 out of 15,902,867
Matches: 81,701 out of 15,902,867
Mismatches: 49,032 out of 15,902,867
Insertions: 12 out of 15,902,867
Identity over aligned base-pairs: 62.5%