Medicago truncatula vs Manihot esculenta LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Manihot esculenta (Manihot esculenta, Manihot_esculenta_v6) 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 truncatulaManihot esculenta
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 224,714 alignment blocks

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

Uncovered: 349,392,271 out of 412,800,391
Covered: 63,408,120 out of 412,800,391

Uncovered: 14,900,418 out of 50,132,764
Matches: 24,071,656 out of 50,132,764
Mismatches: 10,416,141 out of 50,132,764
Insertions: 744,549 out of 50,132,764
Identity over aligned base-pairs: 68.3%

Manihot esculenta

Uncovered: 515,672,130 out of 582,117,524
Covered: 66,445,394 out of 582,117,524

Uncovered: 5,639,729 out of 38,679,430
Matches: 22,923,607 out of 38,679,430
Mismatches: 9,304,188 out of 38,679,430
Insertions: 811,906 out of 38,679,430
Identity over aligned base-pairs: 69.4%

Block size distribution

Size range All 224,714 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,147
11.2 kb
10 bp - 100 bp
30,635
2.0 Mb
8,559
609.8 kb
100 bp - 1 kb
171,404
60.8 Mb
51,027
18.9 Mb
1 kb - 10 kb
20,388
33.7 Mb
24,016
58.6 Mb
10 kb - 100 kb
138
2.9 Mb
775
17.0 Mb
100 kb - 1 Mb
2
209.3 kb
30
4.4 Mb