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Medicago truncatula vs Lathyrus sativus LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Lathyrus sativus (Lathyrus sativus, JIC_Lsat_v2.1.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 113. 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 truncatulaLathyrus sativus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,049,827 alignment blocks

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

Uncovered: 256,621,746 out of 429,196,467
Covered: 172,574,721 out of 429,196,467

Uncovered: 4,052,842 out of 45,081,035
Matches: 34,235,801 out of 45,081,035
Mismatches: 6,081,267 out of 45,081,035
Insertions: 711,125 out of 45,081,035
Identity over aligned base-pairs: 83.4%

Lathyrus sativus

Uncovered: 5,676,828,832 out of 5,967,284,493
Covered: 290,455,661 out of 5,967,284,493

Uncovered: 3,623,111 out of 36,172,806
Matches: 27,881,052 out of 36,172,806
Mismatches: 4,242,791 out of 36,172,806
Insertions: 425,852 out of 36,172,806
Identity over aligned base-pairs: 85.7%

Block size distribution

Size range All 1,049,827 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
9,013
52.8 kb
10 bp - 100 bp
218,407
14.3 Mb
108,515
7.5 Mb
100 bp - 1 kb
741,854
246.3 Mb
450,424
154.7 Mb
1 kb - 10 kb
80,523
132.6 Mb
80,758
171.3 Mb
10 kb - 100 kb
30
424.6 kb
1,154
25.1 Mb
100 kb - 1 Mb
40
10.6 Mb
1 Mb - 10 Mb
9
24.6 Mb