An Macrohap Allele consists of an alleic sequence at variant sites only of forensic CODIS STRs, SNPs and InDels. VarAlleleDB deposits alleles,cross-validated information and their frequency count in human populations. The current version includes two sets of humman samples, each with three databases at population, supperpopulation and global scale, from the 1000 genome project. The coordinate position is based on HG38.
Dataset I: 289 validated individuals; 11,560 alleles.
Dataset II: 2504 unrelated individuals; 100,160 alleles.
Both have 26 populations (FIN,CDX,IBS,MXL,CHB,CHS,CEU,JPT,ESN,KHV,TSI,CLM,YRI,GBR,PEL,STU,BEB,GIH,PJL,MSL,ITU,GWD,LWK,ASW,PUR,ACB), 5 supperpopulations (EAS, EUR, AFR,SAS, AMR).
Either database works. For advanced users, the SQL version is recommended.
This type of database is in TAB separated text files and can be searched and viewed in the Internet browser using the tool provided here.
This type database is in SQL format, which can be searched and used via SQL command. The tables in this MacroHapDB database contain all the files in text format in github, and additional alleles. They are a serial of short MH derived from the full-length macrohap dataset. Each subset MacroHapDB from 289 validated humans are in an separate table in the database named as:
MH289supPop_300
MH289supPop_500
MH289supPop_1000
MH289supPop_1500
MH289supPop_2000
MH289supPop_3000
MH289supPop_4000
MH289supPop_5000
MH289supPop_6000
MH289supPop_7000
MH289supPop_8000
mh289full
There are five columns in each table. The column names ['locus', 'population', 'macrohap', 'count', 'consistency']
The SQL database MacroHapDB.sql is available on request.
The VarAlleleDB can be directly run and viewed in any computer after downloading. No additional installation is required once an internet browser, e.g. Chrome, IE, Edge, firefox etc., is there. Users can use either method to install the database in a computer.
Download the files from github using the following command:
git clone https://github.com/XuewenWangUGA/MacroHapDB
Double click the viewer MacroHapDB_viewer.html in the downloaded folder to run the database.
Download the database compressed files from the github page and uncompress it.
Then, double click the viewer MacroHapDB_viewer.html in the downloaded folder to run the database.
Step 1. choose a database file: .global, pop, superPop
Step 2. select a marker name from drop-down list
Step 3. the alleles for selected marker will be shown up in a Tab separated text.
The displayed alleles for each marker will have five columns, e.g.,
CSF1PO EAS C,C,T,G,C,A,G,C,C,G,A,T,T,C,G,T,A,C,T,T,T,G,C,T,A,G,A,C,C,G,C,C,G,G,G,G,C,T,C,G,G,G,G,G;T,T,G;ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT 136 T=A=S
Meaning of each column:
- column 1 is the marker/locus name, e.g., CSF1PO
- column 2 is the population name, e.g., EAS
- column 3 is the variant allele. SNPs, InDels and STRs separated by ";"
- column 4 is the frequency count of this allele in the given population EAS
- column 5 is the validated consistency information.T=A=S represents a consistency between three mathods.
Each variant is separated by ",". The position of each variant is provided in our Github depository https://github.com/XuewenWangUGA/VarSeqStitcher/tree/main/testData .
Here is an example for load the supper-population database.
Step 1. open the database file "stitched.MH.allele_count.1KG2504.supPop.consisTag.txt"
Step 2. click to choose the marker "CSF1PO" or any other marker name from the drop-down list
the variant allele will be displayed for the selected marker as shown in Fig1.
Fig1.
Command in mysql terminal: mysql> USE MacroHapDB
check the data example
Command: mysql> SELECT * FROM mh289full LIMIT 2;
+--------+------------+-------------------------------------------------------------------------------------------------------------------------------------------------+-------+-------------+
| locus | population | macrohap | count | consistency |
+--------+------------+-------------------------------------------------------------------------------------------------------------------------------------------------+-------+-------------+
| CSF1PO | EAS | C,C,T,G,C,A,G,C,C,G,A,T,T,C,G,T,A,C,T,T,T,G,C,T,A,G,A,C,C,G,C,C,G,G,G,G,C,T,C,G,G,G,G,G;T,T,G;ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT | 17 | T=A=S |
| CSF1PO | EAS | C,C,T,A,C,G,G,C,C,C,A,T,T,C,G,T,A,C,T,T,T,G,C,T,G,A,A,C,C,G,C,C,G,G,G,G,C,T,T,C,G,A,G,G;T,T,GT;ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT | 12 | T=A=S |
+--------+------------+-------------------------------------------------------------------------------------------------------------------------------------------------+-------+-------------+
2 rows in set (0.00 sec)
Search for the MH alleles if TPOX locus with count great than or equal to 10 for Europians, show the top 2 records.
mysql> SELECT macrohap FROM mh289full WHERE locus='TPOX' AND population='EUR' AND count >=10 LIMIT 2;
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| macrohap |
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| A,G,G,A,T,C,G,A,A,T,T,T,A,T,T,G,A,G,G,C,C,C,T,C,G,G,C,T,T,A,G,C,T,G,C,T,C,A,G,C,A,T,T,G,G,C,A,A,C,C,T,G,G,A,A,C,G,G,C,C,G,A,T,G,C,C,G,C,G,A,C,C,C,G,G,A,G,A,G,A,T,A,C,C;C,TAGTGGGG,CAGG,G;AATGAATGAATGAATGAATGAATGAATGAATG |
| A,G,G,A,T,C,G,A,A,T,T,T,A,T,T,G,C,G,G,C,C,C,T,C,G,G,C,T,T,A,G,C,T,G,C,T,C,A,G,C,A,T,T,G,G,C,A,A,C,C,T,G,G,A,A,C,G,G,C,C,C,A,T,G,C,C,G,C,A,A,C,C,C,G,G,A,G,A,G,A,T,A,C,C;C,TAGTGGGG,CAGG,G;AATGAATGAATGAATGAATGAATGAATGAATG |
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
2 rows in set (0.01 sec)
Total count of unique MH alleles passed a threshold:
mysql> SELECT COUNT(macrohap) FROM mh289full WHERE locus='TPOX' AND population='EUR' AND count >=10 ;
+--------------+
| COUNT(macrohap) |
+--------------+
| 4 |
+--------------+
1 row in set (0.02 sec)`
Additional tools for processing and using the database.
A python tool to generate macrohaps for an in silico man with the MacrohapDB alleles. The output is the MH alleles for the in silico man in evidence MH format and suspected MH format.
example:
python freqBasedAllelePicker.py -i MHtest2000.txt -o MH_inSilicoMan
Input libray file is: MHtest2000.txt
Number of simulated DNA contributors: 1
prefix of Output files: MH_inSilicoMan
This is in silico Macrohap alleles maker
Results:
MH allele in evidence format: MH_inSilicoMan.MH.tsv
MH allele in suspect format: MH_inSilicoMan.MHs.tsv
Download the tool and the test data from Util folder and then run the following command:
python freqBasedAllelePicker.py -i MHtest2000.txt -m 1 -o MH_inSilicoMan
Options:
-h, --help: show this help message and exit
-i, --input: a required file of macrohap database
#database format (tab separated):
CSF1PO EAS C,C,T,G,C,A,G;;ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT 29 T=A=S
CSF1PO EAS C,C,T,G,C,A,G;;ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT 28 T=A=S
-m, --mix: integer >=1, the number of individuals in simulated DNA evidenced mixture, default 1
-o, --out, prefix of file name. Results are the tab delimited allele data in evidence and suspect format.
#suspect format (tab separated):
TH01 C,C,T,T,G,T,C,G,G,G,C,C;G;AATGAATGAATGAATGAATGAATGAATG 1
TH01 C,T,C,T,G,T,G,G,G,G,A,C;G;AATGAATGAATGAATGAATGAATG 1
TPOX C,G,A,T,G,C,C,G,C,G,A,C,C,C,G,G,A,G;G;AATGAATGAATGAATGAATGAATGAATGAATG 2
#Evidence format: similar to suspect format but no the 3rd column
Version: 1.0.0, Mar,18th,2024
This work was sponsored in part by award 15PNIJ-21-GG-04159-RESS, awarded by the National Institute of Justice, Office of Justice Programs, U.S. Department of Justice.
Contact: Xuewen.Wang at UNTHSC.edu, August.Woerner at UNTHSC.edu