Medicago truncatula vs Pisum sativum LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Pisum sativum (Pisum sativum, Pisum_sativum_v1a) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 107. 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 truncatulaPisum sativum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 687,622 alignment blocks

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

Uncovered: 261,491,083 out of 412,800,391
Covered: 151,309,308 out of 412,800,391

Uncovered: 7,180,865 out of 50,132,764
Matches: 35,546,908 out of 50,132,764
Mismatches: 6,642,978 out of 50,132,764
Insertions: 762,013 out of 50,132,764
Identity over aligned base-pairs: 82.8%

Pisum sativum

Uncovered: 3,721,159,945 out of 3,920,131,294
Covered: 198,971,349 out of 3,920,131,294

Uncovered: 8,511,436 out of 42,854,030
Matches: 29,253,927 out of 42,854,030
Mismatches: 4,580,366 out of 42,854,030
Insertions: 508,301 out of 42,854,030
Identity over aligned base-pairs: 85.2%

Block size distribution

Size range All 687,622 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
6,797
41.0 kb
10 bp - 100 bp
130,737
8.5 Mb
62,000
4.4 Mb
100 bp - 1 kb
495,986
167.8 Mb
295,525
100.3 Mb
1 kb - 10 kb
53,785
88.6 Mb
48,921
110.7 Mb
10 kb - 100 kb
316
10.0 Mb
2,165
48.4 Mb
100 kb - 1 Mb
1
100.1 kb
40
6.8 Mb
1 Mb - 10 Mb
2
4.5 Mb