Arabidopsis thaliana vs Brassica napus LastZ Results

Back to all analyses

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Brassica napus (Brassica napus, AST_PRJEB5043_v1) 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: 525,856

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

Uncovered: 34,697,339 out of 119,667,750
Covered: 84,970,411 out of 119,667,750

Uncovered: 1,264,636 out of 33,775,569
Matches: 24,107,166 out of 33,775,569
Mismatches: 7,662,498 out of 33,775,569
Insertions: 741,269 out of 33,775,569

Brassica napus

Uncovered: 552,713,876 out of 848,200,303
Covered: 295,486,427 out of 848,200,303

Uncovered: 7,894,629 out of 101,157,402
Matches: 77,965,998 out of 101,157,402
Mismatches: 13,984,775 out of 101,157,402
Insertions: 1,312,000 out of 101,157,402

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 Brassica napus
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}