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Medicago truncatula vs Pisum sativum Garden pea LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Pisum sativum Garden pea (Pisum sativum, CAAS_Psat_ZW6_1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 115. 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 truncatulaPisum sativum Garden pea
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 881,768 alignment blocks

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

Uncovered: 255,779,118 out of 429,196,467
Covered: 173,417,349 out of 429,196,467

Uncovered: 3,879,037 out of 45,081,035
Matches: 34,530,564 out of 45,081,035
Mismatches: 5,985,089 out of 45,081,035
Insertions: 686,345 out of 45,081,035
Identity over aligned base-pairs: 83.8%

Pisum sativum Garden pea

Uncovered: 3,553,388,574 out of 3,796,552,622
Covered: 243,164,048 out of 3,796,552,622

Uncovered: 16,437,496 out of 53,752,548
Matches: 31,763,929 out of 53,752,548
Mismatches: 5,007,776 out of 53,752,548
Insertions: 543,347 out of 53,752,548
Identity over aligned base-pairs: 85.1%

Block size distribution

Size range All 881,768 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
8,010
47.2 kb
10 bp - 100 bp
172,638
11.2 Mb
93,370
6.4 Mb
100 bp - 1 kb
628,557
213.0 Mb
386,654
131.2 Mb
1 kb - 10 kb
72,540
119.4 Mb
67,263
141.7 Mb
10 kb - 100 kb
23
445.6 kb
1,170
27.8 Mb
100 kb - 1 Mb
83
18.6 Mb
1 Mb - 10 Mb
8
18.4 Mb