Arabidopsis thaliana vs Gossypium raimondii LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Gossypium raimondii (Gossypium raimondii, Graimondii2_0) 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: 172,649

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

Uncovered: 80,421,677 out of 119,667,750
Covered: 39,246,073 out of 119,667,750

Uncovered: 7,178,601 out of 33,775,569
Matches: 18,063,666 out of 33,775,569
Mismatches: 7,906,034 out of 33,775,569
Insertions: 627,268 out of 33,775,569

Gossypium raimondii

Uncovered: 704,182,197 out of 761,405,269
Covered: 57,223,072 out of 761,405,269

Uncovered: 9,401,297 out of 45,523,048
Matches: 24,516,513 out of 45,523,048
Mismatches: 10,591,617 out of 45,523,048
Insertions: 1,013,621 out of 45,523,048

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 Gossypium raimondii
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}