Giardia lamblia vs Pythium ultimum Translated Blat results

Giardia lamblia (Giardia lamblia, GL2) 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 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 lambliaPythium 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 1,296 alignment blocks

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

Uncovered: 11,014,003 out of 11,192,215
Covered: 178,212 out of 11,192,215

Uncovered: 9,148,197 out of 9,322,001
Matches: 112,295 out of 9,322,001
Mismatches: 61,485 out of 9,322,001
Insertions: 24 out of 9,322,001
Identity over aligned base-pairs: 64.6%

Pythium ultimum

Uncovered: 44,755,146 out of 44,913,582
Covered: 158,436 out of 44,913,582

Uncovered: 19,685,055 out of 19,826,256
Matches: 90,466 out of 19,826,256
Mismatches: 50,727 out of 19,826,256
Insertions: 8 out of 19,826,256
Identity over aligned base-pairs: 64.1%