1000 Genomes Visualization
The repository contains a program of Web services using the SNP data of 1000 Genomes Project.
Features
- focused on the difference of Genotype frequency by Ethnicity.
Use library
- Python
- Flask
- MySQL.connector
- JavaScript
- jQuery
- jVectorMap
- Highcharts
Version (recommended)
- python 2.7.5
- flask 0.10.1
- MySQL.connector 1.2.2
- jQuery 1.11.0
- jVectorMap 1.2.2
DataBase
OverView
- Engine : InnoDB
- Size : 25.2GiB
- Column : 85,639,460
- Encoding: utf-8
Table design
CREATE TABLE `main` (
`chr` varchar(2) NOT NULL DEFAULT '',
`pos` int(15) NOT NULL,
`id` varchar(15) NOT NULL,
`REF` tinytext NOT NULL,
`ALT` tinytext NOT NULL,
`info` text NOT NULL,
KEY `id` (`id`),
KEY `pos` (`pos`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;Example
| Column | Content |
|---|---|
| chr | 1 |
| pos | 10177 |
| id | . |
| REF | A |
| ALT | AC |
| info | 1|1:23,1|0:29,0|1:28,0|0:33;1|1:9,0|1:34,1|0:20,0|0:31;1|1:28,0|1:15,1|0:27,0|0:16;0|0:19,0|1:30,1|0:26,1|1:10;1|1:9,1|0:37,0|1:36,0|0:17;1|1:35,0|1:19,1|0:24,0|0:7;1|1:3,0|1:21,1|0:31,0|0:36;0|0:34,1|0:23,0|1:42,1|1:8;1|1:2,0|1:15,1|0:23,0|0:21;1|1:4,0|1:26,1|0:24,0|0:45;1|1:21,0|1:39,1|0:42,0|0:5;0|0:38,0|1:28,1|0:29,1|1:4;1|1:7,1|0:36,0|1:38,0|0:18;0|0:13,0|1:43,1|0:41,1|1:11;1|1:1,0|1:38,1|0:30,0|0:34;0|0:16,1|0:30,0|1:36,1|1:20;1|0:21,0|1:22,0|0:62;1|1:30,0|1:26,1|0:28,0|0:15;1|1:12,0|1:26,1|0:30,0|0:28;0|0:19,0|1:24,1|0:40,1|1:20;1|1:8,1|0:26,0|1:28,0|0:34;1|0:19,0|1:20,0|0:25;1|1:18,1|0:32,0|1:38,0|0:14;1|1:10,1|0:16,0|1:13,0|0:54;0|0:13,1|0:40,0|1:30,1|1:21;1|1:6,0|1:24,1|0:27,0|0:47 |
License
Copyright 2014-2016 Yoshihiro Tanaka
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.