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Medicago truncatula vs Cucumis sativus LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Cucumis sativus (Cucumis sativus, ASM407v2) 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 truncatulaCucumis sativus
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 156,335 alignment blocks

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

Uncovered: 362,862,129 out of 412,800,391
Covered: 49,938,262 out of 412,800,391

Uncovered: 18,236,094 out of 50,132,764
Matches: 21,794,099 out of 50,132,764
Mismatches: 9,428,167 out of 50,132,764
Insertions: 674,404 out of 50,132,764
Identity over aligned base-pairs: 68.3%

Cucumis sativus

Uncovered: 157,525,709 out of 193,829,320
Covered: 36,303,611 out of 193,829,320

Uncovered: 4,530,056 out of 26,192,424
Matches: 14,859,146 out of 26,192,424
Mismatches: 6,286,984 out of 26,192,424
Insertions: 516,238 out of 26,192,424
Identity over aligned base-pairs: 68.6%

Block size distribution

Size range All 156,335 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,271
6.5 kb
10 bp - 100 bp
21,898
1.4 Mb
5,982
418.2 kb
100 bp - 1 kb
121,804
41.9 Mb
31,985
12.0 Mb
1 kb - 10 kb
11,342
17.4 Mb
16,990
41.0 Mb
10 kb - 100 kb
20
557.8 kb
412
7.8 Mb
100 kb - 1 Mb
2
219.1 kb