Coverage of genome alligments

Coverage with double selection:



Coverage is 36.0% in 2334 parts with average length 553
RNAcode: sum length genes 427380 299 regions
13% of CDS surface is retrieved









Coverage with distance variation

Coverage old Alligment 20 genomes:



  • 1121114

    Coverage is 24.0% in 7801 parts with average length 184

  • 1316931

    Coverage is 46.8% in 12153 parts with average length 174

  • 206672

    Coverage is 54.5% in 10264 parts with average length 119

  • 226186

    Coverage is 40.1% in 10992 parts with average length 229

  • 411490

    Coverage is 34.1% in 6709 parts with average length 183

  • 445974

    Coverage is 51.3% in 7985 parts with average length 206

  • 511145

    Coverage is 75.2% in 10914 parts with average length 319

  • 525338

    Coverage is 42.8% in 5641 parts with average length 242

Coverage closest collection Alligment 15 genomes:



  • blautia

    Coverage is 34.2% in 6085 parts with average length 350

  • clostri

    Coverage is 51.1% in 9093 parts with average length 264

  • bifi

    Coverage is 67.3% in 3733 parts with average length 406

  • bact

    Coverage is 48.6% in 7868 parts with average length 389

  • anaero

    Coverage is 44.5% in 4115 parts with average length 388

  • ery

    Coverage is 45.6% in 4637 parts with average length 319

  • ecoli

    Coverage is 78.1% in 6511 parts with average length 556

  • lacto

    Coverage is 47.6% in 3665 parts with average length 422

Coverage closest with additiv distance (3) collection Alligment 15 genomes:

  • blautia

    Coverage is 21.0% in 4127 parts with average length 317

  • clostri

    Coverage is 32.1% in 5371 parts with average length 280

  • bifi

    Coverage is 53.6% in 3581 parts with average length 337

  • bact

    Coverage is 32.0% in 5198 parts with average length 388

  • anaero

    Coverage is 34.3% in 4126 parts with average length 298

  • ery

    Coverage is 29.3% in 3648 parts with average length 260

  • ecoli

    Coverage is 65.3% in 5020 parts with average length 604

  • lacto

    Coverage is 41.2% in 3468 parts with average length 385






Coverage with variation of number of genomes 20 to 50 by 5

The selection of genomes was hold constant. Always closest selection.

Must for each species one by one. First genome alligment and than rna code, each takes 1/2 day.

Results are printed in

Clostri

  • 20

    Coverage is 57.9% in 11381 parts with average length 238
    7% of CDS surface is retrieved

  • 25

    Coverage is 59.8% in 13049 parts with average length 215
    6% of CDS surface is retrieved

  • 30

    Coverage is 62.8% in 14344 parts with average length 205
    6% of CDS surface is retrieved

  • 35

    Coverage is 61.2% in 14763 parts with average length 194
    5% of CDS surface is retrieved

  • 40

    Coverage is 60.6% in 15250 parts with average length 186
    6% of CDS surface is retrieved

  • 45

    Coverage is 59.9% in 15772 parts with average length 178
    5% of CDS surface is retrieved

  • 50

    Coverage is 59.1% in 16066 parts with average length 172
    4% of CDS surface is retrieved

Ecoli

  • 20

    Coverage is 80.1% in 7580 parts with average length 490
    27% of CDS surface is retrieved

  • 25

    Coverage is 80.7% in 8702 parts with average length 430
    25% of CDS surface is retrieved

  • 30

    Coverage is 80.8% in 9335 parts with average length 401
    24% of CDS surface is retrieved

  • 35

    Coverage is 80.8% in 10081 parts with average length 371
    22% of CDS surface is retrieved

  • 40

    Coverage is 80.4% in 10761 parts with average length 346
    20% of CDS surface is retrieved

  • 45

    Coverage is 80.6% in 10901 parts with average length 343
    19% of CDS surface is retrieved

  • 50

    Coverage is 80.1% in 11691 parts with average length 318
    17% of CDS surface is retrieved

Ery

  • 20

    Coverage is 47.8% in 5922 parts with average length 261
    4% of CDS surface is retrieved

  • 25

    Coverage is 53.6% in 7484 parts with average length 232
    4% of CDS surface is retrieved

  • 30

    Coverage is 57.4% in 8401 parts with average length 222
    4% of CDS surface is retrieved

  • 35

    Coverage is 56.8% in 8850 parts with average length 208
    4% of CDS surface is retrieved

  • 40

    Coverage is 56.8% in 9308 parts with average length 198
    3% of CDS surface is retrieved

  • 45

    Coverage is 56.7% in 9768 parts with average length 188
    3% of CDS surface is retrieved

  • 50

    Coverage is 56.2% in 9983 parts with average length 182
    3% of CDS surface is retrieved

Lacto

  • 20

    Coverage is 53.0% in 4446 parts with average length 387
    7% of CDS surface is retrieved

  • 25

    Coverage is 55.1% in 5025 parts with average length 356
    7% of CDS surface is retrieved

  • 30

    Coverage is 57.2% in 5438 parts with average length 342
    7% of CDS surface is retrieved

  • 35

    Coverage is 58.5% in 5971 parts with average length 318
    6% of CDS surface is retrieved

  • 40

    Coverage is 61.4% in 6609 parts with average length 302
    6% of CDS surface is retrieved

  • 45

    Coverage is 61.3% in 7120 parts with average length 279
    6% of CDS surface is retrieved

  • 50

    Coverage is 61.6% in 7380 parts with average length 271
    6% of CDS surface is retrieved

Blautia

  • 20

    Coverage is 40.8% in 8777 parts with average length 290
    7% of CDS surface is retrieved

  • 25

    Coverage is 42.5% in 10517 parts with average length 252
    6% of CDS surface is retrieved

  • 30

    Coverage is 44.8% in 11973 parts with average length 233
    6% of CDS surface is retrieved

  • 35

    Coverage is 46.2% in 13006 parts with average length 221
    5% of CDS surface is retrieved

  • 40

    Coverage is 47.0% in 14178 parts with average length 207
    4% of CDS surface is retrieved

  • 45

    Coverage is 47.9% in 15028 parts with average length 198
    5% of CDS surface is retrieved

  • 50

    Coverage is 48.8% in 16453 parts with average length 185
    4% of CDS surface is retrieved






Coverage with variation of number of genomes 8 to 17 by 3

The selection of genomes was hold constant. Always closest selection.

Must for each species one by one. First genome alligment and than rna code, each takes 1/2 day.

Results are printed in

Clostri

Annotation NCBI length: 4730133 (nuc)

  • 8

    Coverage is 39.9% in 4276 parts with average length 437
    RNAcode: sum length genes 519129 387 regions
    11% of CDS surface is retrieved

  • 11

    Coverage is 46.8% in 5928 parts with average length 370
    RNAcode: sum length genes 568983 420 regions
    12% of CDS surface is retrieved

  • 14

    Coverage is 50.2% in 8231 parts with average length 286
    RNAcode: sum length genes 323622 231 regions
    7% of CDS surface is retrieved

  • 17

    Coverage is 52.9% in 10251 parts with average length 242
    RNAcode: sum length genes 284133 199 regions
    6% of CDS surface is retrieved

Ecoli

Annotation NCBI length: 4081934 (nuc)

  • 8

    Coverage is 68.7% in 4112 parts with average length 775
    RNAcode: sum length genes 1299741 (nuc) in 993 regions
    32% of CDS surface is retrieved

  • 11

    Genome coverage is 70.4% in 5161 parts with average length 633
    RNAcode: sum length genes 1198050 (nuc) in 850 regions
    29% of CDS surface is retrieved

  • 14

    Genome coverage is 77.8% in 6337 parts with average length 569
    RNAcode: sum length genes 1212138 (nuc) in 870 regions
    30% of CDS surface is retrieved

  • 17

    Genome coverage is 78.7% in 6969 parts with average length 524
    RNAcode: sum length genes 1137141 (nuc) in 823 regions
    28% of CDS surface is retrieved

Ery

Annotation NCBI length: 2851791 (nuc)

  • 8

    Coverage is 30.0% in 2292 parts with average length 424
    RNAcode: sum length genes 126426 80 regions
    4% of CDS surface is retrieved

  • 11

    Coverage is 33.6% in 3139 parts with average length 348
    RNAcode: sum length genes 103200 66 regions
    4% of CDS surface is retrieved

  • 14

    Coverage is 41.7% in 4328 parts with average length 313
    RNAcode: sum length genes 104523 70 regions
    4% of CDS surface is retrieved

  • 17

    Coverage is 46.4% in 4939 parts with average length 305
    RNAcode: sum length genes 117582 81 regions
    4% of CDS surface is retrieved

Bifi

Annotation NCBI length: 1929312 (nuc)

  • 8

    Genome coverage is 49.6% in 1981 parts with average length 564
    RNAcode: sum length genes 188388 (nuc) in 124 regions
    10% of CDS surface is retrieved

  • 11

    Genome coverage is 62.4% in 2856 parts with average length 493
    RNAcode: sum length genes 317985 (nuc) in 207 regions
    16% of CDS surface is retrieved

  • 14

    Genome coverage is 66.9% in 3636 parts with average length 415
    RNAcode: sum length genes 332766 (nuc) in 212 regions
    17% of CDS surface is retrieved

  • 17

    Genome coverage is 67.5% in 4307 parts with average length 354
    RNAcode: sum length genes 301734 (nuc) in 193 regions
    16% of CDS surface is retrieved

Blautia

Annotation NCBI length: 5487493 (nuc)

  • 8

    Genome coverage is 25.9% in 3026 parts with average length 534
    RNAcode: sum length genes 447402 (nuc) in 319 regions
    8% of CDS surface is retrieved

  • 11

    Genome coverage is 30.6% in 4705 parts with average length 405
    RNAcode: sum length genes 452913 (nuc) in 313 regions
    8% of CDS surface is retrieved

  • 14

    Genome coverage is 32.5% in 5601 parts with average length 361
    RNAcode: sum length genes 436260 (nuc) in 304 regions
    8% of CDS surface is retrieved

  • 17

    Genome coverage is 37.0% in 7059 parts with average length 327
    RNAcode: sum length genes 427257 (nuc) in 303 regions
    8% of CDS surface is retrieved

Lacto

Annotation NCBI length: 5714619 (nuc)

  • 8

    Coverage is 38.9% in 2194 parts with average length 576
    7% of CDS surface is retrieved

  • 11

    Coverage is 43.6% in 2733 parts with average length 518
    7% of CDS surface is retrieved

  • 14

    Coverage is 47.1% in 3408 parts with average length 449
    7% of CDS surface is retrieved

  • 17

    Coverage is 48.1% in 3878 parts with average length 403
    7% of CDS surface is retrieved

Bact

Annotation NCBI length: 5714619 (nuc)

  • 8

    Genome coverage is 41.4% in 4875 parts with average length 535
    RNAcode: sum length genes 575868 (nuc) in 351 regions
    10% of CDS surface is retrieved

  • 11

    Genome coverage is 44.7% in 6473 parts with average length 434
    RNAcode: sum length genes 603576 (nuc) in 370 regions
    11% of CDS surface is retrieved

  • 14

    Genome coverage is 48.1% in 7288 parts with average length 416
    RNAcode: sum length genes 582003 (nuc) in 341 regions
    10% of CDS surface is retrieved

  • 17

    Genome coverage is 50.3% in 9141 parts with average length 346
    RNAcode: sum length genes 549963 (nuc) in 329 regions
    10% of CDS surface is retrieved

Anaero

Annotation NCBI length: 3237807 (nuc)

  • 8

    Coverage is 36.0% in 2334 parts with average length 553
    RNAcode: sum length genes 427380 299 regions
    13% of CDS surface is retrieved

  • 11

    Coverage is 41.3% in 3257 parts with average length 455
    RNAcode: sum length genes 415818 288 regions
    13% of CDS surface is retrieved

  • 14

    Coverage is 43.5% in 3904 parts with average length 399
    RNAcode: sum length genes 406008 285 regions
    13% of CDS surface is retrieved

  • 17

    Coverage is 45.7% in 4570 parts with average length 359
    RNAcode: sum length genes 388602 267 regions
    12% of CDS surface is retrieved