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Phytophthora infestans vs Phytophthora lateralis LastZ results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Phytophthora infestans 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 infestansPhytophthora lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 122,909 alignment blocks

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

Uncovered: 158,172,328 out of 228,543,505
Covered: 70,371,177 out of 228,543,505

Uncovered: 4,085,781 out of 22,421,425
Matches: 13,702,497 out of 22,421,425
Mismatches: 4,361,641 out of 22,421,425
Insertions: 271,506 out of 22,421,425
Identity over aligned base-pairs: 74.7%

Phytophthora lateralis

Uncovered: 12,396,342 out of 43,981,379
Covered: 31,585,037 out of 43,981,379

Uncovered: 970,618 out of 14,242,768
Matches: 9,198,827 out of 14,242,768
Mismatches: 3,834,526 out of 14,242,768
Insertions: 238,797 out of 14,242,768
Identity over aligned base-pairs: 69.3%

Block size distribution

Size range All 122,909 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,437
8.3 kb
10 bp - 100 bp
15,775
1.0 Mb
7,364
517.9 kb
100 bp - 1 kb
83,851
31.9 Mb
44,987
17.0 Mb
1 kb - 10 kb
21,604
44.9 Mb
19,238
47.1 Mb
10 kb - 100 kb
242
3.9 Mb
811
17.0 Mb
100 kb - 1 Mb
1
100.2 kb