Owl/web/nightingales/O_lurida/20160223_gbs

###Directory Contents
---
#### bgi_project_summary (directory)

Project summary files provided by BGI. See [GBS wiki](https://github.com/RobertsLab/project-olympia.oyster-genomic/wiki/Genotype-by-sequencing-November-2015) for detailed project info.

Key files are:

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

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

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

- ```nj_tree.out.tre.svg```: Vector graphic (i.e. special image file) of phylogenetic tree.

#### checksums.md5

MD5 hash file for evaluating file integrity during transfers. Created using OSX md5 command.

#### enzyme.txt

A text file specifically for use in the demultiplexing script (```split.sh```) provided by BGI. Contains the <em>Ape</em>KI restriction site.

#### index.lst

A tab-delimited text file consisting of sample names and corresponding barcode. Needed for demultplexing 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz & 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz using the ```split.sh``` script.

#### md5.txt

MD5 checksums provided by BGI of demultiplexed FASTQ files.

#### md51.txt

MD5 checksums provided by BGI of non-demultiplexed FASTQ files.

Also includes MD5 checksums for index.lst and split.sh. The index.lst file has been changed since receipt, since it was not formatted correctly to use with the split.sh script.
See [Sam's Jupyter Notebook for more info](https://github.com/sr320/LabDocs/blob/master/jupyter_nbs/sam/20170314_docker_Oly_BGI_GBS_demultiplexing_reproducibility.ipynb)

#### oly_gbs_fastqc.tar.gz

A gzipped file containing FastQC reports for all FASTQ files in this directory, excluding the Unknow_1.fq.gz and Unknow_2.fq.gz.

#### split.sh

Script file provided by BGI for adapter removal and demultiplexing 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz & 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz.

---

#### Illumina FASTQ Files

---

Project Summary: Olympia oyster population comparisons using genotype-by-sequencing.

Tissue: whole body

Date Received: 20160223

Notebook(s):http://onsnetwork.org/kubu4/category/olympia-oyster-reciprocal-transplant/genotype-by-sequencing-at-bgi/

Sequencing: BGI

Sequencing Platform: Illumina HiSeq4000

Read Type/Length: 100bp paired-end

Total Number of Files: 194

Total Number of Reads: 557,596,520

Reads Per File:


| 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 |


Raw FASTQ Files

Total Number of Files: 2

Total Number of Reads: 728,522,092

Reads Per File:

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