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Phytophthora ramorum vs Pythium irregulare LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_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 irregulare
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 42,860 alignment blocks

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

Uncovered: 42,166,602 out of 66,652,401
Covered: 24,485,799 out of 66,652,401

Uncovered: 5,906,817 out of 22,377,278
Matches: 11,071,582 out of 22,377,278
Mismatches: 4,922,210 out of 22,377,278
Insertions: 476,669 out of 22,377,278
Identity over aligned base-pairs: 67.2%

Pythium irregulare

Uncovered: 21,624,228 out of 42,968,084
Covered: 21,343,856 out of 42,968,084

Uncovered: 4,160,886 out of 20,543,058
Matches: 10,438,906 out of 20,543,058
Mismatches: 5,210,935 out of 20,543,058
Insertions: 732,331 out of 20,543,058
Identity over aligned base-pairs: 63.7%

Block size distribution

Size range All 42,860 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
159
836.0 bp
10 bp - 100 bp
4,529
305.4 kb
1,216
86.8 kb
100 bp - 1 kb
29,279
12.2 Mb
9,959
4.5 Mb
1 kb - 10 kb
8,853
16.3 Mb
6,760
17.5 Mb
10 kb - 100 kb
40
557.0 kb
425
7.2 Mb