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Medicago truncatula vs Arabidopsis lyrata LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Arabidopsis lyrata (Arabidopsis lyrata subsp. lyrata, v.1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. Medicago truncatula was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

Chunking parameters

ParameterMedicago truncatulaArabidopsis lyrata
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 164,143 alignment blocks

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

Uncovered: 367,330,608 out of 412,800,391
Covered: 45,469,783 out of 412,800,391

Uncovered: 20,212,664 out of 50,132,764
Matches: 19,888,563 out of 50,132,764
Mismatches: 9,258,455 out of 50,132,764
Insertions: 773,082 out of 50,132,764
Identity over aligned base-pairs: 66.5%

Arabidopsis lyrata

Uncovered: 167,532,744 out of 206,667,935
Covered: 39,135,191 out of 206,667,935

Uncovered: 10,006,827 out of 35,389,059
Matches: 16,998,254 out of 35,389,059
Mismatches: 7,798,497 out of 35,389,059
Insertions: 585,481 out of 35,389,059
Identity over aligned base-pairs: 67.0%

Block size distribution

Size range All 164,143 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,543
8.4 kb
10 bp - 100 bp
24,315
1.6 Mb
5,747
406.9 kb
100 bp - 1 kb
126,871
43.2 Mb
34,026
13.2 Mb
1 kb - 10 kb
11,386
17.3 Mb
19,807
45.2 Mb
10 kb - 100 kb
27
947.0 kb
242
4.2 Mb
100 kb - 1 Mb
1
100.0 kb
1
149.6 kb