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Phytophthora ramorum vs Pythium iwayamai LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Phytophthora ramorum was used as the reference species. After running LastZ, the raw LastZ 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
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterPhytophthora ramorumPythium iwayamai
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 49,204 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora ramorum

Uncovered: 42,154,671 out of 66,652,401
Covered: 24,497,730 out of 66,652,401

Uncovered: 6,427,588 out of 22,377,278
Matches: 10,604,849 out of 22,377,278
Mismatches: 4,861,298 out of 22,377,278
Insertions: 483,543 out of 22,377,278
Identity over aligned base-pairs: 66.5%

Pythium iwayamai

Uncovered: 22,446,104 out of 43,199,174
Covered: 20,753,070 out of 43,199,174

Uncovered: 4,098,183 out of 19,552,457
Matches: 9,906,627 out of 19,552,457
Mismatches: 4,905,624 out of 19,552,457
Insertions: 642,023 out of 19,552,457
Identity over aligned base-pairs: 64.1%

Block size distribution

Size range All 49,204 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
164
890.0 bp
10 bp - 100 bp
5,019
339.8 kb
1,540
110.4 kb
100 bp - 1 kb
35,763
14.4 Mb
14,466
6.1 Mb
1 kb - 10 kb
8,227
14.5 Mb
7,718
19.4 Mb
10 kb - 100 kb
31
434.9 kb
278
4.0 Mb