Medicago truncatula vs Vigna angularis LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Vigna angularis (Vigna angularis, Vigan1.1) 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 truncatulaVigna angularis
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 277,593 alignment blocks

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

Uncovered: 319,442,569 out of 412,800,391
Covered: 93,357,822 out of 412,800,391

Uncovered: 10,637,174 out of 50,132,764
Matches: 29,946,365 out of 50,132,764
Mismatches: 8,697,510 out of 50,132,764
Insertions: 851,715 out of 50,132,764
Identity over aligned base-pairs: 75.8%

Vigna angularis

Uncovered: 374,016,953 out of 466,744,453
Covered: 92,727,500 out of 466,744,453

Uncovered: 7,672,875 out of 37,822,470
Matches: 23,250,669 out of 37,822,470
Mismatches: 6,314,411 out of 37,822,470
Insertions: 584,515 out of 37,822,470
Identity over aligned base-pairs: 77.1%

Block size distribution

Size range All 277,593 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,106
18.8 kb
10 bp - 100 bp
43,670
2.7 Mb
16,960
1.2 Mb
100 bp - 1 kb
200,183
75.6 Mb
72,716
24.8 Mb
1 kb - 10 kb
30,513
50.2 Mb
19,230
47.1 Mb
10 kb - 100 kb
120
2.8 Mb
826
20.7 Mb
100 kb - 1 Mb
1
100.4 kb
100
24.8 Mb
1 Mb - 10 Mb
8
12.8 Mb