Difference between revisions of "Texas Xenopus Genome Project/XENLA SA09023"
From Marcotte Lab
(→WG_5kb) |
(→BAC_2kb_F3) |
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+ | == Overall == | ||
+ | * [[xdata:XENLA_seq.20091211.SA09023_Qscore.pdf]] | ||
+ | |||
== BAC_2kb == | == BAC_2kb == | ||
* Sequencing 96 BAC clones from CHORI-219, with 2kb mate-pair library construction. | * Sequencing 96 BAC clones from CHORI-219, with 2kb mate-pair library construction. | ||
Line 14: | Line 17: | ||
** After 35 bp : 945,355 | ** After 35 bp : 945,355 | ||
** Before 35 bp : 386,928 | ** Before 35 bp : 386,928 | ||
+ | * Reads without repeats (pBACGK1.1 + RepBase 15.05) : 34,079,501 (expected coverage: 177x) | ||
* '''Reads with average Qscore >= 15 : 20,607,858''' | * '''Reads with average Qscore >= 15 : 20,607,858''' | ||
* Reads with minimum Qscore >= 15 : 379,916 | * Reads with minimum Qscore >= 15 : 379,916 | ||
Line 27: | Line 31: | ||
** After 35 bp : 827,335 | ** After 35 bp : 827,335 | ||
** Before 35 bp : 294,577 | ** Before 35 bp : 294,577 | ||
+ | * Reads without repeats (pBACGK1.1 + RepBase 15.05) : 34,246,323 (expected coverage: 177x) | ||
* '''Reads with average Qscore >= 15 : 22,050,059''' | * '''Reads with average Qscore >= 15 : 22,050,059''' | ||
* Reads with minimum Qscore >= 15 : 1,549,458 | * Reads with minimum Qscore >= 15 : 1,549,458 | ||
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** SA09023_MPQuad_X_laevis_WB_R3_QV.qual (6.7 GB; 1.9 GB gzipped) | ** SA09023_MPQuad_X_laevis_WB_R3_QV.qual (6.7 GB; 1.9 GB gzipped) | ||
− | * Total reads: 44,888, | + | * Total reads: 44,888,428 |
* Reads without no-call ('.' in .csfasta, '-1' in .qual) : 44,518,144 | * Reads without no-call ('.' in .csfasta, '-1' in .qual) : 44,518,144 | ||
* Reads with no-call : 370,284 | * Reads with no-call : 370,284 | ||
Line 92: | Line 97: | ||
* '''Reads with average Qscore >= 15 : 34,733,020''' | * '''Reads with average Qscore >= 15 : 34,733,020''' | ||
* Reads with minimum Qscore >= 15 : 3,013,026 | * Reads with minimum Qscore >= 15 : 3,013,026 | ||
+ | |||
+ | ---- | ||
+ | [[Category:XenopusGenome]] |
Latest revision as of 13:22, 14 June 2010
Contents |
Overall
BAC_2kb
- Sequencing 96 BAC clones from CHORI-219, with 2kb mate-pair library construction.
- xdata:XENLA_seq.20091124.BAC_2kb_rmapper.pdf
- xdata:XENLA_seq.20091124.BAC_2kb_matepair.pdf
BAC_2kb_F3
- Files
- SA09023_MPQuad_X_laevis_2kb_F3.csfasta (2.4 GB; 672 MB gzipped)
- SA09023_MPQuad_X_laevis_2kb_F3_QV.qual (5.2 GB; 1.5 GB gzipped)
- Total reads: 35,938,421
- Reads without no-call ('.' in .csfasta, '-1' in .qual) : 34,606,138
- Reads with no-call : 1,333,283
- After 35 bp : 945,355
- Before 35 bp : 386,928
- Reads without repeats (pBACGK1.1 + RepBase 15.05) : 34,079,501 (expected coverage: 177x)
- Reads with average Qscore >= 15 : 20,607,858
- Reads with minimum Qscore >= 15 : 379,916
BAC_2kb_R3
- Files
- SA09023_MPQuad_X_laevis_2kb_R3.csfasta (2.4 GB; 689 MB gzipped)
- SA09023_MPQuad_X_laevis_2kb_R3_QV.qual (5.2 GB; 1.5 GB gzipped)
- Total reads: 36,077,234
- Reads without no-call ('.' in .csfasta, '-1' in .qual) : 34,955,322
- Reads with no-call : 1,121,912
- After 35 bp : 827,335
- Before 35 bp : 294,577
- Reads without repeats (pBACGK1.1 + RepBase 15.05) : 34,246,323 (expected coverage: 177x)
- Reads with average Qscore >= 15 : 22,050,059
- Reads with minimum Qscore >= 15 : 1,549,458
BAC_5kb
- Sequencing 96 BAC clones from CHORI-219, with 5kb mate-pair library construction.
- xdata:XENLA_seq.20091124.BAC_5kb_rmapper.pdf
- xdata:XENLA_seq.20091124.BAC_5kb_matepair.pdf
BAC_5kb_F3
- Files
- SA09023_MPQuad_X_laevis_5kb_F3.csfasta (1.8 GB; 449 MB gzipped)
- SA09023_MPQuad_X_laevis_5kb_F3_QV.qual (4.0 GB; 1.2 GB gzipped)
- Total reads: 27,718,394
- Reads without no-call ('.' in .csfasta, '-1' in .qual) : 27,326,849
- Reads with no-call : 391,545
- After 35 bp : 20,043
- Before 35 bp : 371,502
- Reads with average Qscore >= 15 : 14,285,096
- Reads with minimum Qscore >= 15 : 142,514
BAC_5kb_R3
- Files
- SA09023_MPQuad_X_laevis_5kb_R3.csfasta (1.8 GB; 487 MB gzipped)
- SA09023_MPQuad_X_laevis_5kb_R3_QV.qual (3.9 GB; 1.2 GB gzipped)
- Total reads: 27,719,040
- Reads without no-call ('.' in .csfasta, '-1' in .qual) : 27,465,570
- Reads with no-call : 253,470
- After 35 bp : 14,338
- Before 35 bp : 239,132
- Reads with average Qscore >= 15 : 12,236,521
- Reads with minimum Qscore >= 15 : 493,814
WG_5kb
- Sequencing whole genome from X. laevis strain J (MHC inbred), with 5kb mate-pair library construction.
- xdata:XENLA_seq.20091124.WG_5kb_rmapper.pdf
- xdata:XENLA_seq.20091124.WG_5kb_matepair.pdf
- An alternate mapping to the X. tropicalis genome: xdata:xlaevis to trop histogram.pdf
- Also check xdata:XENLA_seq.20091203.WG_5kb_XENTR.pdf
WG_5kb_F3
- Files
- SA09023_MPQuad_X_laevis_WB_F3.csfasta (2.9 GB; 856 MB gzipped)
- SA09023_MPQuad_X_laevis_WB_F3_QV.qual (6.6 GB; 1.9 GB gzipped)
- Total reads: 44,817,834
- Reads without no-call ('.' in .csfasta, '-1' in .qual) : 44,289,548
- Reads with no-call : 528,286
- After 35 bp : 30,381
- Before 35 bp : 497,905
- Reads with average Qscore >= 15 : 31,955,422
- Reads with minimum Qscore >= 15 : 1,226,050
WG_5kb_R3
- Files
- SA09023_MPQuad_X_laevis_WB_R3.csfasta (2.9 GB; 859 MB gzipped)
- SA09023_MPQuad_X_laevis_WB_R3_QV.qual (6.7 GB; 1.9 GB gzipped)
- Total reads: 44,888,428
- Reads without no-call ('.' in .csfasta, '-1' in .qual) : 44,518,144
- Reads with no-call : 370,284
- After 35 bp : 4,962
- Before 35 bp : 365,322
- Reads with average Qscore >= 15 : 34,733,020
- Reads with minimum Qscore >= 15 : 3,013,026