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Medicago truncatula vs Phaseolus vulgaris LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Phaseolus vulgaris (Phaseolus vulgaris, PhaVulg1_0) 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 truncatulaPhaseolus vulgaris
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 288,768 alignment blocks

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

Uncovered: 316,448,526 out of 412,800,391
Covered: 96,351,865 out of 412,800,391

Uncovered: 10,475,191 out of 50,132,764
Matches: 30,054,350 out of 50,132,764
Mismatches: 8,742,729 out of 50,132,764
Insertions: 860,494 out of 50,132,764
Identity over aligned base-pairs: 75.8%

Phaseolus vulgaris

Uncovered: 418,133,900 out of 521,076,696
Covered: 102,942,796 out of 521,076,696

Uncovered: 2,242,829 out of 34,663,348
Matches: 25,105,215 out of 34,663,348
Mismatches: 6,689,286 out of 34,663,348
Insertions: 626,018 out of 34,663,348
Identity over aligned base-pairs: 77.4%

Block size distribution

Size range All 288,768 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,208
19.5 kb
10 bp - 100 bp
43,071
2.6 Mb
16,557
1.1 Mb
100 bp - 1 kb
207,470
78.7 Mb
75,038
25.5 Mb
1 kb - 10 kb
34,842
58.2 Mb
22,788
54.9 Mb
10 kb - 100 kb
177
3.6 Mb
773
18.0 Mb
100 kb - 1 Mb
66
21.6 Mb
1 Mb - 10 Mb
12
22.1 Mb