Bigelowiella natans vs Albugo laibachii Translated Blat results

Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) 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 75. Bigelowiella natans 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

ParameterBigelowiella natansAlbugo 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 6,154 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Bigelowiella natans

Uncovered: 94,008,453 out of 94,701,163
Covered: 692,710 out of 94,701,163

Uncovered: 28,149,382 out of 28,817,508
Matches: 442,645 out of 28,817,508
Mismatches: 225,436 out of 28,817,508
Insertions: 45 out of 28,817,508
Identity over aligned base-pairs: 66.3%

Albugo laibachii

Uncovered: 32,211,988 out of 32,766,811
Covered: 554,823 out of 32,766,811

Uncovered: 15,373,797 out of 15,902,867
Matches: 348,202 out of 15,902,867
Mismatches: 180,804 out of 15,902,867
Insertions: 64 out of 15,902,867
Identity over aligned base-pairs: 65.8%