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Medicago truncatula vs Vigna radiata LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Vigna radiata (Vigna radiata var. radiata, Vradiata_ver6) 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 radiata
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 347,033 alignment blocks

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

Uncovered: 314,483,266 out of 412,800,391
Covered: 98,317,125 out of 412,800,391

Uncovered: 10,304,323 out of 50,132,764
Matches: 29,866,271 out of 50,132,764
Mismatches: 9,092,013 out of 50,132,764
Insertions: 870,157 out of 50,132,764
Identity over aligned base-pairs: 75.0%

Vigna radiata

Uncovered: 346,917,182 out of 463,085,359
Covered: 116,168,177 out of 463,085,359

Uncovered: 2,519,836 out of 36,130,572
Matches: 25,676,798 out of 36,130,572
Mismatches: 7,264,417 out of 36,130,572
Insertions: 669,521 out of 36,130,572
Identity over aligned base-pairs: 76.4%

Block size distribution

Size range All 347,033 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,368
20.5 kb
10 bp - 100 bp
63,059
4.0 Mb
33,417
2.3 Mb
100 bp - 1 kb
244,040
89.8 Mb
106,889
36.3 Mb
1 kb - 10 kb
36,400
61.6 Mb
25,869
60.8 Mb
10 kb - 100 kb
166
3.6 Mb
841
19.4 Mb
100 kb - 1 Mb
80
20.7 Mb
1 Mb - 10 Mb
10
19.7 Mb