Giardia lamblia vs Hyaloperonospora arabidopsidis Translated Blat Results

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Giardia lamblia (Giardia lamblia, GL2) and Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Giardia lamblia was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 935

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

Uncovered: 11,055,304 out of 11,192,215
Covered: 136,911 out of 11,192,215

Uncovered: 9,186,980 out of 9,322,001
Matches: 87,287 out of 9,322,001
Mismatches: 47,722 out of 9,322,001
Insertions: 12 out of 9,322,001

Hyaloperonospora arabidopsidis

Uncovered: 78,775,446 out of 78,897,814
Covered: 122,368 out of 78,897,814

Uncovered: 13,056,587 out of 13,171,834
Matches: 73,902 out of 13,171,834
Mismatches: 41,324 out of 13,171,834
Insertions: 21 out of 13,171,834

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

Giardia lamblia Hyaloperonospora arabidopsidis
Chunk size 1,000,000 1,000,000
Overlap 10,000 10,000
Group set size 100,000,000 100,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}