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Phytophthora ramorum vs Giardia intestinalis - GCA_000002435.2 LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis, GCA000002435v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 114. 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 ramorumGiardia intestinalis - GCA_000002435.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,706 alignment blocks

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

Uncovered: 65,952,061 out of 66,652,401
Covered: 700,340 out of 66,652,401

Uncovered: 21,757,506 out of 22,377,278
Matches: 368,147 out of 22,377,278
Mismatches: 228,308 out of 22,377,278
Insertions: 23,317 out of 22,377,278
Identity over aligned base-pairs: 59.4%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,626,305 out of 12,078,186
Covered: 451,881 out of 12,078,186

Uncovered: 9,031,553 out of 9,469,365
Matches: 234,297 out of 9,469,365
Mismatches: 183,507 out of 9,469,365
Insertions: 20,008 out of 9,469,365
Identity over aligned base-pairs: 53.5%

Block size distribution

Size range All 1,706 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3
19.0 bp
10 bp - 100 bp
231
16.9 kb
120
9.0 kb
100 bp - 1 kb
1,284
492.8 kb
775
341.1 kb
1 kb - 10 kb
187
294.9 kb
228
454.5 kb
10 kb - 100 kb
1
13.3 kb
1
13.3 kb