In this section

Medicago truncatula vs Phaseolus vulgaris LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Phaseolus vulgaris (Phaseolus vulgaris, PhaVulg1_0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 112. 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 truncatulaPhaseolus vulgaris
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 317,900 alignment blocks

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

Uncovered: 326,882,225 out of 429,196,467
Covered: 102,314,242 out of 429,196,467

Uncovered: 7,772,892 out of 45,081,035
Matches: 28,337,161 out of 45,081,035
Mismatches: 8,161,548 out of 45,081,035
Insertions: 809,434 out of 45,081,035
Identity over aligned base-pairs: 76.0%

Phaseolus vulgaris

Uncovered: 409,489,986 out of 521,076,696
Covered: 111,586,710 out of 521,076,696

Uncovered: 2,928,963 out of 34,663,348
Matches: 24,627,280 out of 34,663,348
Mismatches: 6,472,692 out of 34,663,348
Insertions: 634,413 out of 34,663,348
Identity over aligned base-pairs: 77.6%

Block size distribution

Size range All 317,900 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,431
20.4 kb
10 bp - 100 bp
50,152
3.1 Mb
22,263
1.5 Mb
100 bp - 1 kb
224,789
84.4 Mb
88,800
30.1 Mb
1 kb - 10 kb
39,345
67.2 Mb
26,965
66.2 Mb
10 kb - 100 kb
182
3.3 Mb
742
16.7 Mb
100 kb - 1 Mb
1
119.0 kb
67
21.7 Mb
1 Mb - 10 Mb
12
21.9 Mb