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Phytophthora infestans vs Guillardia theta CCMP2712 LastZ results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. 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 infestansGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 9,203 alignment blocks

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

Uncovered: 225,831,832 out of 228,543,505
Covered: 2,711,673 out of 228,543,505

Uncovered: 20,216,915 out of 22,421,425
Matches: 1,336,786 out of 22,421,425
Mismatches: 775,704 out of 22,421,425
Insertions: 92,020 out of 22,421,425
Identity over aligned base-pairs: 60.6%

Guillardia theta CCMP2712

Uncovered: 84,843,247 out of 87,266,873
Covered: 2,423,626 out of 87,266,873

Uncovered: 28,589,530 out of 30,644,092
Matches: 1,194,120 out of 30,644,092
Mismatches: 774,011 out of 30,644,092
Insertions: 86,431 out of 30,644,092
Identity over aligned base-pairs: 58.1%

Block size distribution

Size range All 9,203 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
38
172.0 bp
10 bp - 100 bp
1,997
138.6 kb
444
32.1 kb
100 bp - 1 kb
6,425
2.2 Mb
3,168
1.3 Mb
1 kb - 10 kb
733
1.2 Mb
1,080
2.0 Mb
10 kb - 100 kb
10
213.8 kb
22
393.2 kb