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Medicago truncatula vs Pisum sativum JI2822 LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Pisum sativum JI2822 (Pisum sativum, JIC_Psat_v1.3) 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 JI2822
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,024,802 alignment blocks

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

Uncovered: 253,116,614 out of 429,196,467
Covered: 176,079,853 out of 429,196,467

Uncovered: 3,837,883 out of 45,081,035
Matches: 34,571,476 out of 45,081,035
Mismatches: 5,982,744 out of 45,081,035
Insertions: 688,932 out of 45,081,035
Identity over aligned base-pairs: 83.8%

Pisum sativum JI2822

Uncovered: 3,539,174,958 out of 3,842,015,444
Covered: 302,840,486 out of 3,842,015,444

Uncovered: 2,328,765 out of 38,789,482
Matches: 31,543,960 out of 38,789,482
Mismatches: 4,441,754 out of 38,789,482
Insertions: 475,003 out of 38,789,482
Identity over aligned base-pairs: 86.5%

Block size distribution

Size range All 1,024,802 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
9,131
52.9 kb
10 bp - 100 bp
210,985
13.6 Mb
117,830
8.0 Mb
100 bp - 1 kb
717,177
242.4 Mb
445,841
151.7 Mb
1 kb - 10 kb
87,308
149.9 Mb
80,522
171.8 Mb
10 kb - 100 kb
201
2.5 Mb
1,582
36.5 Mb
100 kb - 1 Mb
104
22.5 Mb
1 Mb - 10 Mb
8
18.0 Mb