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Oryza sativa Japonica Group vs Musa acuminata LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Musa acuminata (Musa acuminata subsp. malaccensis, Musa_acuminata_v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 104. Oryza sativa Japonica Group 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

ParameterOryza sativa Japonica GroupMusa acuminata
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 173,703 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 334,724,957 out of 375,049,285
Covered: 40,324,328 out of 375,049,285

Uncovered: 10,012,096 out of 34,424,450
Matches: 16,466,246 out of 34,424,450
Mismatches: 7,208,416 out of 34,424,450
Insertions: 737,692 out of 34,424,450
Identity over aligned base-pairs: 67.5%

Musa acuminata

Uncovered: 405,439,322 out of 450,848,473
Covered: 45,409,151 out of 450,848,473

Uncovered: 9,878,093 out of 41,197,995
Matches: 21,483,197 out of 41,197,995
Mismatches: 9,019,970 out of 41,197,995
Insertions: 816,735 out of 41,197,995
Identity over aligned base-pairs: 68.6%

Block size distribution

Size range All 173,703 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,718
8.1 kb
10 bp - 100 bp
26,230
1.8 Mb
6,233
444.7 kb
100 bp - 1 kb
133,855
45.1 Mb
36,691
14.8 Mb
1 kb - 10 kb
11,899
17.7 Mb
22,680
48.4 Mb
10 kb - 100 kb
1
10.2 kb
79
982.6 kb