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Medicago truncatula vs Prunus persica LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Prunus persica (Prunus persica, Prunus_persica_NCBIv2) 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 truncatulaPrunus persica
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 184,223 alignment blocks

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

Uncovered: 355,079,975 out of 412,800,391
Covered: 57,720,416 out of 412,800,391

Uncovered: 14,868,815 out of 50,132,764
Matches: 24,670,538 out of 50,132,764
Mismatches: 9,887,114 out of 50,132,764
Insertions: 706,297 out of 50,132,764
Identity over aligned base-pairs: 70.0%

Prunus persica

Uncovered: 179,058,169 out of 227,411,381
Covered: 48,353,212 out of 227,411,381

Uncovered: 5,795,499 out of 33,236,255
Matches: 18,981,372 out of 33,236,255
Mismatches: 7,745,413 out of 33,236,255
Insertions: 713,971 out of 33,236,255
Identity over aligned base-pairs: 69.2%

Block size distribution

Size range All 184,223 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,661
8.9 kb
10 bp - 100 bp
26,830
1.7 Mb
8,123
577.8 kb
100 bp - 1 kb
140,258
49.1 Mb
39,383
13.9 Mb
1 kb - 10 kb
15,419
24.3 Mb
15,898
38.0 Mb
10 kb - 100 kb
54
1.3 Mb
529
12.0 Mb
100 kb - 1 Mb
1
100.0 kb
54
12.0 Mb