Oryza sativa Japonica Group vs Marchantia polymorpha LastZ results
Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Marchantia polymorpha (Marchantia polymorpha str. Tak-1, Marchanta_polymorpha_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 97. 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
Parameter | Value |
---|---|
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
Parameter | Oryza sativa Japonica Group | Marchantia polymorpha |
---|---|---|
Chunk size | 10,000,000 | 10,100,000 |
Overlap | 0 | 100,000 |
Group set size | 0 | 10,100,000 |
Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 78,298 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Oryza sativa Japonica Group |
Uncovered: 357,794,314 out of 375,049,285 |
Uncovered: 22,357,423 out of 34,349,962 |
Marchantia polymorpha |
Uncovered: 214,634,878 out of 225,760,816 |
Uncovered: 15,426,974 out of 23,498,831 |
Block size distribution
Size range | All 78,298 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 381 |
1.8 kb |
|||
10 bp - 100 bp | 16,450 |
1.2 Mb |
2,911 |
213.2 kb |
|
100 bp - 1 kb | 59,385 |
16.5 Mb |
17,563 |
7.2 Mb |
|
1 kb - 10 kb | 2,055 |
2.9 Mb |
7,064 |
13.1 Mb |
|
10 kb - 100 kb | 27 |
476.6 kb |
30 |
592.7 kb |