Medicago truncatula vs Brassica napus LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Brassica napus (Brassica napus, AST_PRJEB5043_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Medicago truncatula 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: 403,390

Genome coverage (bp) Coding exon coverage (bp)
Medicago truncatula

Uncovered: 355,594,792 out of 412,800,391
Covered: 57,205,599 out of 412,800,391

Uncovered: 19,210,398 out of 50,132,764
Matches: 19,694,652 out of 50,132,764
Mismatches: 10,304,478 out of 50,132,764
Insertions: 923,236 out of 50,132,764

Brassica napus

Uncovered: 730,521,989 out of 848,200,303
Covered: 117,678,314 out of 848,200,303

Uncovered: 30,305,197 out of 101,157,402
Matches: 47,690,345 out of 101,157,402
Mismatches: 21,687,058 out of 101,157,402
Insertions: 1,474,802 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

Medicago truncatula 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}