Arabidopsis thaliana vs Camelina sativa LastZ Results

Back to all analyses

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Camelina sativa (Camelina sativa, Cs) 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: 586,919

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

Uncovered: 25,428,715 out of 119,667,750
Covered: 94,239,035 out of 119,667,750

Uncovered: 677,188 out of 33,775,569
Matches: 27,221,534 out of 33,775,569
Mismatches: 5,522,491 out of 33,775,569
Insertions: 354,356 out of 33,775,569

Camelina sativa

Uncovered: 307,128,401 out of 641,356,059
Covered: 334,227,658 out of 641,356,059

Uncovered: 9,788,254 out of 107,028,261
Matches: 85,431,311 out of 107,028,261
Mismatches: 10,482,856 out of 107,028,261
Insertions: 1,325,840 out of 107,028,261

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 Camelina sativa
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 10,100,000 10,100,000
Masking options