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Genotype by sequencing November 2015

kubu4 edited this page Apr 19, 2017 · 19 revisions

Progress of high-throughput genotype-by-sequencing (GBS), and analysis, of three distinct populations of Olympia oysters (Ostrea lurida) raised in Oyster Bay.


Manuscript(s):

  • PREPRINT: Genotoype-by-sequencing of three geographically distinct populations of Olympia oysters, Ostrea lurida (2017) White, S.J., Vadopalas, B., Silliman, K., Roberts S.B. Scientific Data

    Preprint (PDF): https://osf.io/cdj7m/
    status


Notebook(s):
Discussions:
Sample collection date(s), sample tissue(s), storage method, storage location, personnel:
  • 20151124, whole body, frozen @ -80C, stored @ -80c (entirety of samples were sent for sequencing), Steven/Brent/Jake
Sample(s):

1NF1A - INF36A (Originated from North Sound/Fidalgo Bay)

1SN1A - 1SN36A (Originated from South Sound/Oyster Bay)

1HL1A - 1HL36A (Originated from Hood Canal/Dabob Bay)

DNA extraction date(s), tissue(s), method(s), and personnel:

Performed by BGI.

DNA Isolation Method: Salting Out (Proteinase K digestion, followed by sodium acetate and EtOH precip)

Library construction date(s) and personnel:

Performed by BGI.

Digestion: ApeKI (NEB)

Library: Illumina libraries. QC via Bioanalyzer (Agilent) and qPCR (ABI).


Sequencing Details

Sequencing:
  • BGI
    • HiSeq4000
    • 100bp PE
    • Insert size 219bp
Sample submission date(s):
QC Report(s) and brief summaries:
  • 20160105_F15FTSUSAT0768_QC_Report.pdf

  • Sequenced the following samples - selected based on QC report:

      1NF1A, INF2A, INF4A - INF33A
    
      1SN1A - 1SN32A
    
      1HL1A - 1HL17A, 1HL19A - 1HL29A, 1HL31A, 1HL33A - 1HL35A
    
  • BGI demultiplexing was performed using Reseqtools with this script: split.sh

  • Demultiplexing requires the following two files:

    index.lst - A tab-delimited text file consisting of sample names and corresponding barcode. Needed for demultplexing using the split.sh script.

    enzyme.txt - A text file containing the restriction cut site for ApeKI. Formatted for use with the split.sh script.

  • Project Summary Files: bgi_gbs_project_summary

    Here is a list of the key files contained in the Project Summary directory:

    • Data.stat.xls: Spreadsheet detailing number of reads generated, number of bases sequenced, GC percentage, Q20 percentage, and Q30 percentage for each individual.

    • Genotype.xls: Spreadsheet providing consensus sequences of genomic regions containing SNPs across individuals; effectively provides a genotype for each individual.

    • SNP.readme_en.txt: A readme file describing the columns in the SNP.stat.csv file.

    • SNP.stat.xls: Spreadsheet summarizing total number of SNPs identified in each individual, as well as breakdown of homozygous/heteroyzgous SNP composition in each individual.

    • genotype.noref.readme_en.txt: A readme file describing the columns in the Genotype.xls file.

    • nj_tree.out.tre.png: A low resolution PNG image of phylogenetic tree of all individual oysters, generated using the Neighbor-Joining method.

    • nj_tree.out.tre.svg: A scalable SVG of phylogenetic tree of all individual oysters, generated using the Neighbor-Joining method. Can be used to create higher resolution image (compared to the nj_tree.out.tre.png file) of the phylogenetic tree. The tree was generated using the software TreeBeST with the following parameters: nj -b 100 snp.fa
      nj: build neighbour-joining tree, SDI, rooting
      -b 100: bootstrapping times

Data receipt date(s), format(s), description, and storage location:

Received: 20160422

Total number of files: 2

Format: FASTQ

Notes:

  • These are the raw FASTQ files.

Location: http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/

Files:

Raw FASTQ Files

Received: 20160422

Total number of files: 2

Format: FASTQ

Location: http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/

FILENAME READS
160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz 364261046
160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz 364261046

Demultioplexed FASTQ Files

Received: 20160223

Total number of files: 194

Format: FASTQ

Location: http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/

Files:

FILENAME READS
1HL_10A_1.fq.gz 3186565
1HL_10A_2.fq.gz 3186565
1HL_11A_1.fq.gz 3568503
1HL_11A_2.fq.gz 3568503
1HL_12A_1.fq.gz 2524813
1HL_12A_2.fq.gz 2524813
1HL_13A_1.fq.gz 2676425
1HL_13A_2.fq.gz 2676425
1HL_14A_1.fq.gz 2015611
1HL_14A_2.fq.gz 2015611
1HL_15A_1.fq.gz 2196324
1HL_15A_2.fq.gz 2196324
1HL_16A_1.fq.gz 2333158
1HL_16A_2.fq.gz 2333158
1HL_17A_1.fq.gz 3653761
1HL_17A_2.fq.gz 3653761
1HL_19A_1.fq.gz 3617984
1HL_19A_2.fq.gz 3617984
1HL_1A_1.fq.gz 2260430
1HL_1A_2.fq.gz 2260430
1HL_20A_1.fq.gz 2908938
1HL_20A_2.fq.gz 2908938
1HL_21A_1.fq.gz 2591845
1HL_21A_2.fq.gz 2591845
1HL_22A_1.fq.gz 2074229
1HL_22A_2.fq.gz 2074229
1HL_23A_1.fq.gz 3609794
1HL_23A_2.fq.gz 3609794
1HL_24A_1.fq.gz 2721808
1HL_24A_2.fq.gz 2721808
1HL_25A_1.fq.gz 2957874
1HL_25A_2.fq.gz 2957874
1HL_26A_1.fq.gz 3142369
1HL_26A_2.fq.gz 3142369
1HL_27A_1.fq.gz 3199649
1HL_27A_2.fq.gz 3199649
1HL_28A_1.fq.gz 3770238
1HL_28A_2.fq.gz 3770238
1HL_29A_1.fq.gz 3071205
1HL_29A_2.fq.gz 3071205
1HL_2A_1.fq.gz 2758150
1HL_2A_2.fq.gz 2758150
1HL_31A_1.fq.gz 2453753
1HL_31A_2.fq.gz 2453753
1HL_33A_1.fq.gz 2708943
1HL_33A_2.fq.gz 2708943
1HL_34A_1.fq.gz 2899019
1HL_34A_2.fq.gz 2899019
1HL_35A_1.fq.gz 2630313
1HL_35A_2.fq.gz 2630313
1HL_3A_1.fq.gz 2211401
1HL_3A_2.fq.gz 2211401
1HL_4A_1.fq.gz 2571031
1HL_4A_2.fq.gz 2571031
1HL_5A_1.fq.gz 1980666
1HL_5A_2.fq.gz 1980666
1HL_6A_1.fq.gz 2070051
1HL_6A_2.fq.gz 2070051
1HL_7A_1.fq.gz 2793544
1HL_7A_2.fq.gz 2793544
1HL_8A_1.fq.gz 2544013
1HL_8A_2.fq.gz 2544013
1HL_9A_1.fq.gz 2832945
1HL_9A_2.fq.gz 2832945
1NF_10A_1.fq.gz 2149301
1NF_10A_2.fq.gz 2149301
1NF_11A_1.fq.gz 2266647
1NF_11A_2.fq.gz 2266647
1NF_12A_1.fq.gz 2179923
1NF_12A_2.fq.gz 2179923
1NF_13A_1.fq.gz 3890118
1NF_13A_2.fq.gz 3890118
1NF_14A_1.fq.gz 2719198
1NF_14A_2.fq.gz 2719198
1NF_15A_1.fq.gz 2554324
1NF_15A_2.fq.gz 2554324
1NF_16A_1.fq.gz 2682948
1NF_16A_2.fq.gz 2682948
1NF_17A_1.fq.gz 3119328
1NF_17A_2.fq.gz 3119328
1NF_18A_1.fq.gz 1750070
1NF_18A_2.fq.gz 1750070
1NF_19A_1.fq.gz 2036640
1NF_19A_2.fq.gz 2036640
1NF_1A_1.fq.gz 1355760
1NF_1A_2.fq.gz 1355760
1NF_20A_1.fq.gz 2457026
1NF_20A_2.fq.gz 2457026
1NF_21A_1.fq.gz 3046937
1NF_21A_2.fq.gz 3046937
1NF_22A_1.fq.gz 2895176
1NF_22A_2.fq.gz 2895176
1NF_23A_1.fq.gz 3206742
1NF_23A_2.fq.gz 3206742
1NF_24A_1.fq.gz 3038626
1NF_24A_2.fq.gz 3038626
1NF_25A_1.fq.gz 2203229
1NF_25A_2.fq.gz 2203229
1NF_26A_1.fq.gz 2934794
1NF_26A_2.fq.gz 2934794
1NF_27A_1.fq.gz 2272652
1NF_27A_2.fq.gz 2272652
1NF_28A_1.fq.gz 2344763
1NF_28A_2.fq.gz 2344763
1NF_29A_1.fq.gz 3829981
1NF_29A_2.fq.gz 3829981
1NF_2A_1.fq.gz 3452931
1NF_2A_2.fq.gz 3452931
1NF_30A_1.fq.gz 2701047
1NF_30A_2.fq.gz 2701047
1NF_31A_1.fq.gz 3561574
1NF_31A_2.fq.gz 3561574
1NF_32A_1.fq.gz 3477986
1NF_32A_2.fq.gz 3477986
1NF_33A_1.fq.gz 2602951
1NF_33A_2.fq.gz 2602951
1NF_4A_1.fq.gz 3582899
1NF_4A_2.fq.gz 3582899
1NF_5A_1.fq.gz 2765984
1NF_5A_2.fq.gz 2765984
1NF_6A_1.fq.gz 2423888
1NF_6A_2.fq.gz 2423888
1NF_7A_1.fq.gz 2590507
1NF_7A_2.fq.gz 2590507
1NF_8A_1.fq.gz 2772580
1NF_8A_2.fq.gz 2772580
1NF_9A_1.fq.gz 3380498
1NF_9A_2.fq.gz 3380498
1SN_10A_1.fq.gz 2558667
1SN_10A_2.fq.gz 2558667
1SN_11A_1.fq.gz 2583992
1SN_11A_2.fq.gz 2583992
1SN_12A_1.fq.gz 3423902
1SN_12A_2.fq.gz 3423902
1SN_13A_1.fq.gz 2956991
1SN_13A_2.fq.gz 2956991
1SN_14A_1.fq.gz 3544290
1SN_14A_2.fq.gz 3544290
1SN_15A_1.fq.gz 2506325
1SN_15A_2.fq.gz 2506325
1SN_16A_1.fq.gz 2616966
1SN_16A_2.fq.gz 2616966
1SN_17A_1.fq.gz 2983401
1SN_17A_2.fq.gz 2983401
1SN_18A_1.fq.gz 3248512
1SN_18A_2.fq.gz 3248512
1SN_19A_1.fq.gz 3036463
1SN_19A_2.fq.gz 3036463
1SN_1A_1.fq.gz 3040537
1SN_1A_2.fq.gz 3040537
1SN_20A_1.fq.gz 2155177
1SN_20A_2.fq.gz 2155177
1SN_21A_1.fq.gz 3540618
1SN_21A_2.fq.gz 3540618
1SN_22A_1.fq.gz 3060365
1SN_22A_2.fq.gz 3060365
1SN_23A_1.fq.gz 3696257
1SN_23A_2.fq.gz 3696257
1SN_24A_1.fq.gz 1885265
1SN_24A_2.fq.gz 1885265
1SN_25A_1.fq.gz 3037089
1SN_25A_2.fq.gz 3037089
1SN_26A_1.fq.gz 2758873
1SN_26A_2.fq.gz 2758873
1SN_27A_1.fq.gz 2607809
1SN_27A_2.fq.gz 2607809
1SN_28A_1.fq.gz 2841587
1SN_28A_2.fq.gz 2841587
1SN_29A_1.fq.gz 2257274
1SN_29A_2.fq.gz 2257274
1SN_2A_1.fq.gz 3080107
1SN_2A_2.fq.gz 3080107
1SN_30A_1.fq.gz 3840203
1SN_30A_2.fq.gz 3840203
1SN_31A_1.fq.gz 3353715
1SN_31A_2.fq.gz 3353715
1SN_32A_1.fq.gz 2552635
1SN_32A_2.fq.gz 2552635
1SN_3A_1.fq.gz 2442489
1SN_3A_2.fq.gz 2442489
1SN_4A_1.fq.gz 3294871
1SN_4A_2.fq.gz 3294871
1SN_5A_1.fq.gz 3000852
1SN_5A_2.fq.gz 3000852
1SN_6A_1.fq.gz 3354310
1SN_6A_2.fq.gz 3354310
1SN_7A_1.fq.gz 2964594
1SN_7A_2.fq.gz 2964594
1SN_8A_1.fq.gz 3269810
1SN_8A_2.fq.gz 3269810
1SN_9A_1.fq.gz 3177205
1SN_9A_2.fq.gz 3177205
UnKnow_1.fq.gz 7344729
UnKnow_2.fq.gz 7344729
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