Bigelowiella natans vs Phytophthora ramorum Translated Blat results

Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) and Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) 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 natansPhytophthora ramorum
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 7,858 alignment blocks

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

Uncovered: 93,852,259 out of 94,701,163
Covered: 848,904 out of 94,701,163

Uncovered: 28,000,938 out of 28,817,508
Matches: 547,821 out of 28,817,508
Mismatches: 268,674 out of 28,817,508
Insertions: 75 out of 28,817,508
Identity over aligned base-pairs: 67.1%

Phytophthora ramorum

Uncovered: 65,954,085 out of 66,652,401
Covered: 698,316 out of 66,652,401

Uncovered: 21,698,435 out of 22,377,278
Matches: 453,158 out of 22,377,278
Mismatches: 225,586 out of 22,377,278
Insertions: 99 out of 22,377,278
Identity over aligned base-pairs: 66.8%