Data from: Intra-individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it?

Scarcelli N, Mariac C, Couvreur TLP, Faye A, Richard D, Sabot F, Berthouly-Salazar C, Vigouroux Y

Date Published: September 14, 2015

DOI: http://dx.doi.org/10.5061/dryad.31733

 

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Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title A571_Run4-TAG-10
Downloaded 3 times
Description Dioscorea abyssinica A571 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
Download A571_Run4-R1-TAG-10.bam (89.92 Mb)
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Title A571_Run7-TAG-9
Downloaded 4 times
Description Dioscorea abyssinica A571 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
Download A571_Run7-R1-TAG-9.bam (32.37 Mb)
Details View File Details
Title A571_RunHi-TAG-9
Downloaded 2 times
Description Dioscorea abyssinica A571 sample - Whole genome sequencing (HiSeq) - .bam file containing reads after mapping on the chloroplast genome
Download A571_RunHi-R1-TAG-9.bam (145.0 Mb)
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Title CR659_Run10-TAG-70
Downloaded 4 times
Description Dioscorea rotundata CR659 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
Download CR659_Run10-R1-TAG-70.bam (23.35 Mb)
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Title P458_Run4-TAG-25
Downloaded 2 times
Description Dioscorea praehensilis P458 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
Download P458_Run4-R1-TAG-25.bam (65.26 Mb)
Details View File Details
Title Pa-Mayo9-R11T57_R1R2.fastq
Downloaded 3 times
Description Podococcus acaulis Pa-Mayoko9 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
Download Pa-Mayo9-R11T57_R1R2.fastq.bam (99.17 Mb)
Details View File Details
Title Pa-Ndjo3-R11T18_R1R2.fastq
Downloaded 2 times
Description Podococcus acaulis Pa-Ndjo3 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
Download Pa-Ndjo3-R11T18_R1R2.fastq.bam (38.72 Mb)
Details View File Details
Title Pa-Ndjo9-R11T16_R1R2.fastq
Downloaded 2 times
Description Podococcus acaulis Pa-Ndjo9 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
Download Pa-Ndjo9-R11T16_R1R2.fastq.bam (47.52 Mb)
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Title Pa-Ndjo11-R11T19_R1R2.fastq
Downloaded 4 times
Description Podococcus barteri Pb-Ndjo11 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
Download Pa-Ndjo11-R11T19_R1R2.fastq.bam (67.27 Mb)
Details View File Details
Title Pb-Aloum8-R11T73_R1R2.fastq
Downloaded 2 times
Description Podococcus barteri Pb-Aloum8 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
Download Pb-Aloum8-R11T73_R1R2.fastq.bam (74.94 Mb)
Details View File Details
Title Pb-Campo1-R11T81_R1R2.fastq
Downloaded 2 times
Description Podococcus barteri Pb-Campo1 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
Download Pb-Campo1-R11T81_R1R2.fastq.bam (86.90 Mb)
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Title Pb-Kola5-R11T54_R1R2.fastq
Downloaded 2 times
Description Podococcus barteri Pb-Kola5 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
Download Pb-Kola5-R11T54_R1R2.fastq.bam (42.23 Mb)
Details View File Details
Title Pb-Oyem-R11T47_R1R2.fastq
Downloaded 3 times
Description Podococcus barteri Pb-Oyem sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
Download Pb-Oyem-R11T47_R1R2.fastq.bam (43.51 Mb)
Details View File Details
Title Pb-Podo5-1-R2T53_R1R2.fastq
Downloaded 3 times
Description Podococcus barteri Podo 5-1 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
Download Pb-Podo5-1-R2T53_R1R2.fastq.bam (535.9 Kb)
Details View File Details
Title Pb-Podo5-R11T79_R1R2.fastq
Downloaded 2 times
Description Podococcus barteri Podo 5 sample - Long range PCR sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
Download Pb-Podo5-R11T79_R1R2.fastq.bam (17.13 Mb)
Details View File Details
Title TOG6208_mt_Run1-TAG-1
Downloaded 3 times
Description O. glaberrima TOG6028 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the mitochondrial genome. Only reads properly mapped on the chloroplast genome were used.
Download TOG6208_mt_Run1-TAG-1.bam (1.588 Mb)
Details View File Details
Title TOG6208_mt_Run1-TAG-6
Downloaded 4 times
Description O. glaberrima TOG6028 sample - LR-PCR sequencing (MiSeq) - .bam file containing reads after mapping on the mitochondrial genome. Only reads properly mapped on the chloroplast genome were used.
Download TOG6208_mt_Run1-TAG-6.bam (10.72 Mb)
Details View File Details
Title TOG6208_mt_Run1-TAG-LR
Downloaded 3 times
Description O. glaberrima TOG6028 sample - LR-PCR (MiSeq) - .bam file containing reads after mapping on the mitochondrial genome. Only reads properly mapped on the chloroplast genome were used.
Download TOG6208_mt_Run1-TAG-LR.bam (33.41 Mb)
Details View File Details
Title TOG6208_nr_Run1-TAG-1
Downloaded 4 times
Description O. glaberrima TOG6028 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the nuclear genome. Only reads properly mapped on the chloroplast genome were used.
Download TOG6208_nr_Run1-TAG-1.bam (8.800 Mb)
Details View File Details
Title TOG6208_nr_Run1-TAG-6
Downloaded 4 times
Description O. glaberrima TOG6028 sample - Chloroplast enrichment (MiSeq) - .bam file containing reads after mapping on the nuclear genome. Only reads properly mapped on the chloroplast genome were used.
Download TOG6208_nr_Run1-TAG-6.bam (57.21 Mb)
Details View File Details
Title TOG6208_nr_Run1-TAG-LR
Downloaded 5 times
Description O. glaberrima TOG6028 sample - LR-PCR (MiSeq) - .bam file containing reads after mapping on the nuclear genome. Only reads properly mapped on the chloroplast genome were used.
Download TOG6208_nr_Run1-TAG-LR.bam (421.7 Kb)
Details View File Details
Title TOG6208_cp_RUN1_TAG1
Downloaded 5 times
Description O. glaberrima TOG6028 sample - genomic library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used.
Download TOG6208_cp_RUN1_TAG1.bam (11.95 Mb)
Details View File Details
Title TOG6208_cp_RUN1-TAG2-4_10-12.bam
Downloaded 5 times
Description O. glaberrima TOG6028 sample - LRPCR library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used.
Download TOG6208_cp_RUN1-AG2-4_10-12.bam (13.30 Mb)
Details View File Details
Title TOG6208_cp_RUN1_TAG6
Downloaded 4 times
Description O. glaberrima TOG6028 sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used.
Download TOG6208_cp_RUN1_TAG6.bam (13.39 Mb)
Details View File Details
Title PE08106-E1_cp_RUN5-TAG35
Downloaded 3 times
Description Pennisetum glaucum PE08106-E1 sample - genomic library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used.
Download PE08106-E1_cp_RUN5-TAG35.bam (10.17 Mb)
Details View File Details
Title RUN2_TAG32
Downloaded 1 time
Description Pennisetum glaucum PE11356 sample - LRPCR library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used.
Download RUN2_TAG32.bam (8.033 Mb)
Details View File Details
Title RUN2_TAG11-20
Downloaded 2 times
Description Dioscorea rotundata_CR629_sample - genomic library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used.
Download RUN2_TAG11-20.bam (9.340 Mb)
Details View File Details
Title RUN4_TAG-27
Downloaded 4 times
Download RUN4_TAG-27.bam (7.357 Mb)
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Title RUN4_TAG28
Downloaded 3 times
Download RUN4_TAG28.bam (7.303 Mb)
Details View File Details
Title RUN4_TAG29
Downloaded 2 times
Download RUN4_TAG29.bam (7.459 Mb)
Details View File Details
Title RUN4_TAG24
Downloaded 2 times
Download RUN4_TAG24.bam (7.353 Mb)
Details View File Details
Title RUN4_TAG26
Downloaded 3 times
Download RUN4_TAG26.bam (7.532 Mb)
Details View File Details
Title RUN4_TAG-12.bam
Downloaded 2 times
Description Dioscorea praehensilis_P603_sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used.
Download RUN4_TAG-12.bam (7.071 Mb)
Details View File Details
Title RUN4_TAG25
Downloaded 3 times
Description Dioscorea praehensilis_P458_sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used.
Download RUN4_TAG25.bam (7.238 Mb)
Details View File Details
Title RUN4_TAG30
Downloaded 4 times
Description Dioscorea praehensilis_A571_sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used.
Download RUN4_TAG30.bam (7.234 Mb)
Details View File Details
Title RUN3-TAG-55_R2_paired
Downloaded 1 time
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download RUN3-TAG-55_R2_paired.fastq (57.88 Mb)
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Title RUN3-TAG-55_R1_paired
Downloaded 3 times
Download RUN3-TAG-55_R1_paired.fastq (56.00 Mb)
Details View File Details
Title RUN3-TAG-56_R1_paired
Downloaded 3 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download RUN3-TAG-56_R1_paired.fastq (97.81 Mb)
Details View File Details
Title RUN3-TAG-56_R2_paired
Downloaded 4 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download RUN3-TAG-56_R2_paired.fastq (101.0 Mb)
Details View File Details
Title RUN5-TAG35_R1_paired.fastq
Downloaded 7 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download RUN5-TAG35_R1_paired.fastq.gz (1.415 Gb)
Details View File Details
Title RUN5-TAG35_R2_paired.fastq
Downloaded 5 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download RUN5-TAG35_R2_paired.fastq.gz (1.357 Gb)
Details View File Details
Title RUN3-TAG-57_R1_paired
Downloaded 2 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download RUN3-TAG-57_R1_paired.fastq (79.97 Mb)
Details View File Details
Title RUN3-TAG-57_R2_paired
Downloaded 1 time
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download RUN3-TAG-57_R2_paired.fastq (82.65 Mb)
Details View File Details
Title RUN3-TAG-59_R1_paired
Downloaded 2 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download RUN3-TAG-59_R1_paired.fastq (73.39 Mb)
Details View File Details
Title RUN3-TAG-59_R2_paired
Downloaded 2 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download RUN3-TAG-59_R2_paired.fastq (75.84 Mb)
Details View File Details
Title RUN3-TAG-65_R1_paired
Downloaded 3 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download RUN3-TAG-65_R1_paired.fastq (33.10 Mb)
Details View File Details
Title RUN3-TAG-65_R2_paired
Downloaded 2 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download RUN3-TAG-65_R2_paired.fastq (34.21 Mb)
Details View File Details
Title RUN3-TAG-66_R1_paired
Downloaded 3 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download RUN3-TAG-66_R1_paired.fastq (53.85 Mb)
Details View File Details
Title RUN3-TAG-66_R2_paired
Downloaded 2 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download RUN3-TAG-66_R2_paired.fastq (55.63 Mb)
Details View File Details
Title RUN3-TAG-67_R1_paired
Downloaded 2 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download RUN3-TAG-67_R1_paired.fastq (40.78 Mb)
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Title RUN3-TAG-67_R2_paired
Downloaded 2 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download RUN3-TAG-67_R2_paired.fastq (42.13 Mb)
Details View File Details
Title RUN3-TAG-70_R1_paired
Downloaded 2 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download RUN3-TAG-70_R1_paired.fastq (68.48 Mb)
Details View File Details
Title RUN3-TAG-70_R2_paired
Downloaded 2 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download RUN3-TAG-70_R2_paired.fastq (70.76 Mb)
Details View File Details
Title RUN3-TAG-55
Downloaded 2 times
Description Pennisetum glaucum 18311 sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used
Download RUN3-TAG-55.bam (7.005 Mb)
Details View File Details
Title RUN3-TAG-56
Downloaded 3 times
Description Pennisetum glaucum 18945 sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used
Download RUN3-TAG-56.bam (6.869 Mb)
Details View File Details
Title RUN3-TAG-57
Downloaded 4 times
Description Pennisetum glaucum 19529 sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used
Download RUN3-TAG-57.bam (6.934 Mb)
Details View File Details
Title RUN3-TAG-59
Downloaded 2 times
Description Pennisetum glaucum 9024 sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used
Download RUN3-TAG-59.bam (7.073 Mb)
Details View File Details
Title RUN3-TAG-65
Downloaded 3 times
Description Pennisetum glaucum PE01514 sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used
Download RUN3-TAG-65.bam (7.078 Mb)
Details View File Details
Title RUN3-TAG-66
Downloaded 3 times
Description Pennisetum glaucum PE02747 sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used
Download RUN3-TAG-66.bam (7.038 Mb)
Details View File Details
Title RUN3-TAG-67
Downloaded 3 times
Description Pennisetum glaucum PE05720 sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used
Download RUN3-TAG-67.bam (7.023 Mb)
Details View File Details
Title RUN3-TAG-70
Downloaded 2 times
Description Pennisetum glaucum PE05727 sample - chloroplast enrichment library (MiSeq) - .bam file containing reads after mapping on the chloroplast genome. Only reads properly mapped were used
Download RUN3-TAG-70.bam (6.988 Mb)
Details View File Details
Title filtcutRUN4-TAG-12_R1_paired
Downloaded 3 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download filtcutRUN4-TAG-12_R1_paired.fastq (342.9 Mb)
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Title filtcutRUN4-TAG-12_R2_paired
Downloaded 3 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download filtcutRUN4-TAG-12_R2_paired.fastq (354.5 Mb)
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Title filtcutRUN4-TAG-24_R1_paired
Downloaded 3 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download filtcutRUN4-TAG-24_R1_paired.fastq (57.50 Mb)
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Title filtcutRUN4-TAG-24_R2_paired
Downloaded 2 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download filtcutRUN4-TAG-24_R2_paired.fastq (59.42 Mb)
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Title filtcutRUN4-TAG-25_R1_paired
Downloaded 3 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download filtcutRUN4-TAG-25_R1_paired.fastq (167.6 Mb)
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Title filtcutRUN4-TAG-26_R1_paired
Downloaded 3 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download filtcutRUN4-TAG-26_R1_paired.fastq (36.50 Mb)
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Title filtcutRUN4-TAG-25_R2_paired
Downloaded 2 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download filtcutRUN4-TAG-25_R2_paired.fastq (173.2 Mb)
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Title filtcutRUN4-TAG-26_R2_paired
Downloaded 3 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download filtcutRUN4-TAG-26_R2_paired.fastq (37.72 Mb)
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Title filtcutRUN4-TAG-27_R1_paired
Downloaded 3 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download filtcutRUN4-TAG-27_R1_paired.fastq (69.56 Mb)
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Title filtcutRUN4-TAG-27_R2_paired
Downloaded 3 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download filtcutRUN4-TAG-27_R2_paired.fastq (71.87 Mb)
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Title filtcutRUN4-TAG-28_R1_paired
Downloaded 1 time
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download filtcutRUN4-TAG-28_R1_paired.fastq (55.75 Mb)
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Title filtcutRUN4-TAG-29_R1_paired
Downloaded 4 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download filtcutRUN4-TAG-29_R1_paired.fastq (22.78 Mb)
Details View File Details
Title filtcutRUN4-TAG-28_R2_paired
Downloaded 1 time
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download filtcutRUN4-TAG-28_R2_paired.fastq (57.61 Mb)
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Title filtcutRUN4-TAG-29_R2_paired
Downloaded 4 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download filtcutRUN4-TAG-29_R2_paired.fastq (23.54 Mb)
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Title filtcutRUN4-TAG-30_R1_paired
Downloaded 3 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download filtcutRUN4-TAG-30_R1_paired.fastq (160.4 Mb)
Details View File Details
Title filtcutRUN4-TAG-30_R2_paired
Downloaded 2 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download filtcutRUN4-TAG-30_R2_paired.fastq (165.7 Mb)
Details View File Details
Title filtcutRUN4-TAG-31_R1_paired
Downloaded 2 times
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download filtcutRUN4-TAG-31_R1_paired.fastq (40.81 Mb)
Details View File Details
Title filtcutRUN4-TAG-31_R2_paired
Downloaded 1 time
Description Fastq data : see sup. table 1 (MER-15-0195) for more details
Download filtcutRUN4-TAG-31_R2_paired.fastq (42.18 Mb)
Details View File Details
Title Dioscorea_Bcf
Downloaded 3 times
Description vcf produce when calling SNP on Dioscorea samples with Bcf method
Download Dioscorea_Bcf.vcf (4.740 Mb)
Details View File Details
Title Dioscorea_Bcf_A571
Downloaded 3 times
Description vcf produce when calling SNP on Dioscorea abyssinica samples with Bcf method
Download Dioscorea_Bcf_A571.vcf (4.832 Mb)
Details View File Details
Title Dioscorea_BcfB
Downloaded 3 times
Description vcf produce when calling SNP on Dioscorea samples with BcfB method
Download Dioscorea_BcfB.vcf (12.57 Mb)
Details View File Details
Title Dioscorea_BcfB_A571
Downloaded 2 times
Description vcf produce when calling SNP on Dioscorea abyssinica samples with BcfB method
Download Dioscorea_BcfB_A571.vcf (12.87 Mb)
Details View File Details
Title Dioscorea_BVar15
Downloaded 3 times
Description vcf produce when calling SNP on Dioscorea samples with BVar15 method
Download Dioscorea_BVar15.vcf (7.266 Mb)
Details View File Details
Title Dioscorea_BVar15_A571
Downloaded 1 time
Description vcf produce when calling SNP on Dioscorea abyssinica samples with BVar15 method
Download Dioscorea_BVar15_A571.vcf (7.509 Mb)
Details View File Details
Title Dioscorea_BVar50
Downloaded 2 times
Description vcf produce when calling SNP on Dioscorea samples with BVar50 method
Download Dioscorea_BVar50.vcf (5.708 Mb)
Details View File Details
Title Dioscorea_BVar50_A571
Downloaded 4 times
Description vcf produce when calling SNP on Dioscorea abyssinica samples with BVar50 method
Download Dioscorea_BVar50_A571.vcf (5.890 Mb)
Details View File Details
Title Dioscorea_Hap
Downloaded 2 times
Description vcf produce when calling SNP on Dioscorea samples with Hap method
Download Dioscorea_Hap.vcf (9.033 Mb)
Details View File Details
Title Dioscorea_Hap_A571
Downloaded 1 time
Description vcf produce when calling SNP on Dioscorea abyssinica samples with Hap method
Download Dioscorea_Hap_A571.vcf (9.206 Mb)
Details View File Details
Title Dioscorea_Uni
Downloaded 4 times
Description vcf produce when calling SNP on Dioscorea samples with Uni method
Download Dioscorea_Uni.vcf (14.96 Mb)
Details View File Details
Title Dioscorea_Uni1
Downloaded 1 time
Description vcf produce when calling SNP on Dioscorea samples with Uni1 method
Download Dioscorea_Uni1.vcf (3.946 Mb)
Details View File Details
Title Dioscorea_Uni1_A571
Downloaded 2 times
Description vcf produce when calling SNP on Dioscorea abyssinica samples with Uni1 method
Download Dioscorea_Uni1_A571.vcf (4.070 Mb)
Details View File Details
Title Dioscorea_Uni_A571
Downloaded 3 times
Description vcf produce when calling SNP on Dioscorea abyssinica samples with Uni method
Download Dioscorea_Uni_A571.vcf (15.39 Mb)
Details View File Details
Title Dioscorea_Var15
Downloaded 3 times
Description vcf produce when calling SNP on Dioscorea samples with Var15 method
Download Dioscorea_Var15.vcf (1.471 Mb)
Details View File Details
Title Dioscorea_Var15_A571
Downloaded 1 time
Description vcf produce when calling SNP on Dioscorea abyssinica samples with Var15 method
Download Dioscorea_Var15_A571.vcf (1.517 Mb)
Details View File Details
Title Dioscorea_Var50
Downloaded 2 times
Description vcf produce when calling SNP on Dioscorea samples with Var50 method
Download Dioscorea_Var50.vcf (1.213 Mb)
Details View File Details
Title Dioscorea_Var50_A571
Downloaded 2 times
Description vcf produce when calling SNP on Dioscorea abyssinica samples with Var50 method
Download Dioscorea_Var50_A571.vcf (1.250 Mb)
Details View File Details
Title SNP_mil_HET50-MINFREQ-15
Downloaded 2 times
Description vcf produce when calling SNP on Pennisetum glaucum (enriched, genomic and LRPCR libraries) with Mpileup -Bg and Varscan (min_freq_for_hom =0.5 and --min-var-freq 0.15)
Download SNP_mil_HET50-MINFREQ-15.VCF (37.61 Kb)
Details View File Details
Title SNP_PODO_HET50-MINFREQ-15
Downloaded 2 times
Description vcf produce when calling SNP on Podoccocus ssp. (enriched, genomic and LRPCR libraries) with Mpileup -Bg and Varscan (min_freq_for_hom =0.5 and --min-var-freq 0.15)
Download SNP_PODO_HET50-MINFREQ-15.VCF (378.3 Kb)
Details View File Details
Title SNP_yam_HET50-MINFREQ-15
Downloaded 3 times
Description vcf produce when calling SNP on Dioscorea (enriched, genomic and LRPCR libraries) with Mpileup -Bg and Varscan (min_freq_for_hom =0.5 and --min-var-freq 0.15)
Download SNP_yam_HET50-MINFREQ-15.VCF (337.7 Kb)
Details View File Details
Title SNP_rice_HET50-MINFREQ-0
Downloaded 2 times
Description n calling SNP on Oryza glaberima (enriched, genomic and LRPCR libraries) with Mpileup -Bg and Varscan (min_freq_for_hom =0.5 and --min-var-freq 0)
Download SNP_rice_HET50-MINFREQ-0.VCF (109.2 Kb)
Details View File Details
Title SNP_rice_HET50-MINFREQ-5
Downloaded 3 times
Description n calling SNP on Oryza glaberima (enriched, genomic and LRPCR libraries) with Mpileup -Bg and Varscan (min_freq_for_hom =0.5 and --min-var-freq 5 )
Download SNP_rice_HET50-MINFREQ-5.VCF (103.0 Kb)
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Title SNP_rice_HET50-MINFREQ-10
Downloaded 3 times
Description n calling SNP on Oryza glaberima (enriched, genomic and LRPCR libraries) with Mpileup -Bg and Varscan (min_freq_for_hom =0.5 and --min-var-freq 10)
Download SNP_rice_HET50-MINFREQ-10.VCF (63.1 Kb)
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Title SNP_rice_HET50-MINFREQ-15
Downloaded 5 times
Description n calling SNP on Oryza glaberima (enriched, genomic and LRPCR libraries) with Mpileup -Bg and Varscan (min_freq_for_hom =0.5 and --min-var-freq 15 )
Download SNP_rice_HET50-MINFREQ-15.VCF (49.97 Kb)
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When using this data, please cite the original publication:

Scarcelli N, Mariac C, Couvreur TLP, Faye A, Richard D, Sabot F, Berthouly-Salazar C, Vigouroux Y (2015) Intra-individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it? Molecular Ecology Resources 16(2): 434-445. http://dx.doi.org/10.1111/1755-0998.12462

Additionally, please cite the Dryad data package:

Scarcelli N, Mariac C, Couvreur TLP, Faye A, Richard D, Sabot F, Berthouly-Salazar C, Vigouroux Y (2015) Data from: Intra-individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it? Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.31733
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