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Medicago truncatula vs Pisum sativum LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Pisum sativum (Pisum sativum, Pisum_sativum_v1a) 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 truncatulaPisum sativum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 838,882 alignment blocks

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

Uncovered: 253,753,617 out of 429,196,467
Covered: 175,442,850 out of 429,196,467

Uncovered: 3,854,314 out of 45,081,035
Matches: 34,321,403 out of 45,081,035
Mismatches: 6,197,595 out of 45,081,035
Insertions: 707,723 out of 45,081,035
Identity over aligned base-pairs: 83.3%

Pisum sativum

Uncovered: 3,692,381,589 out of 3,920,131,294
Covered: 227,749,705 out of 3,920,131,294

Uncovered: 8,373,471 out of 42,854,030
Matches: 29,436,802 out of 42,854,030
Mismatches: 4,527,351 out of 42,854,030
Insertions: 516,406 out of 42,854,030
Identity over aligned base-pairs: 85.4%

Block size distribution

Size range All 838,882 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7,743
45.8 kb
10 bp - 100 bp
161,884
10.5 Mb
87,533
6.0 Mb
100 bp - 1 kb
599,624
203.8 Mb
367,392
124.6 Mb
1 kb - 10 kb
69,601
114.8 Mb
66,775
148.5 Mb
10 kb - 100 kb
30
518.6 kb
1,988
40.0 Mb
100 kb - 1 Mb
34
6.0 Mb
1 Mb - 10 Mb
2
4.5 Mb