Arabidopsis thaliana vs Nymphaea colorata LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Nymphaea colorata (Nymphaea colorata, ASM883128v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Arabidopsis thaliana was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 124,664

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 92,800,036 out of 119,667,750
Covered: 26,867,714 out of 119,667,750

Uncovered: 13,227,019 out of 33,775,569
Matches: 13,484,707 out of 33,775,569
Mismatches: 6,649,126 out of 33,775,569
Insertions: 414,717 out of 33,775,569

Nymphaea colorata

Uncovered: 379,671,897 out of 408,396,728
Covered: 28,724,831 out of 408,396,728

Uncovered: 14,970,404 out of 32,910,518
Matches: 11,613,093 out of 32,910,518
Mismatches: 5,855,253 out of 32,910,518
Insertions: 471,768 out of 32,910,518

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
Other parameters (other)--ambiguous=iupac

Chunking parameters

Arabidopsis thaliana Nymphaea colorata
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 10,100,000 10,100,000
Masking options