Medicago truncatula vs Gossypium raimondii LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Gossypium raimondii (Gossypium raimondii, Graimondii2_0) 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: 243,130

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

Uncovered: 353,223,802 out of 412,800,391
Covered: 59,576,589 out of 412,800,391

Uncovered: 15,116,121 out of 50,132,764
Matches: 23,919,020 out of 50,132,764
Mismatches: 10,275,211 out of 50,132,764
Insertions: 822,412 out of 50,132,764

Gossypium raimondii

Uncovered: 691,887,527 out of 761,405,269
Covered: 69,517,742 out of 761,405,269

Uncovered: 6,932,334 out of 45,523,048
Matches: 26,693,156 out of 45,523,048
Mismatches: 10,966,174 out of 45,523,048
Insertions: 931,384 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

Medicago truncatula 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}