SAM是Sequence Alignment/Map 的缩写。像bwa等软件序列比对结果都会输出这样的文件。samtools网站上有专门的文档介绍SAM文件。具体地址：http://samtools.sourceforge.net/SAM1.pdf

很多人困惑SAM文件中的第二列FLAG值是什么意思。根据文档介绍我们可以计算，但是为了方便大家，下面给大家提供一个脚本工具，大家直接输入flag值就可以知道它代表的含义了。

该脚本的使用方法如下截图所示：

脚本工具的使用方法：

将下面的代码保存在记事本里面，另存为一个html文件，如文件名：FlagExplain.html(拓展名一定要为.html)。双击既可以在浏览器里面打开了。

Explain SAM Flags

lstFlags = [["read paired", 0x1],

["read mapped in proper pair", 0x2],

["read unmapped", 0x4],

["mate unmapped", 0x8],

["read reverse strand", 0x10],

["mate reverse strand", 0x20],

["first in pair", 0x40],

["second in pair", 0x80],

["not primary alignment", 0x100],

["read fails platform/vendor quality checks", 0x200],

["read is PCR or optical duplicate", 0x400]];

function explainFlags() {

var flagValue = parseInt(document.getElementById('tb').value); //returns 0 or NaN if can't parse

var summary = "";

for(var i = 0; i < lstFlags.length; i++) {

var checkbox = document.getElementById('cb' + i)

if(lstFlags[i][1] & flagValue) {

summary += "     " + lstFlags[i][0] + "
";

checkbox.checked = true;

} else {

checkbox.checked = false;

}

}

document.getElementById('summary').innerHTML = summary;

}

function checkboxClicked() {

//compute the new flag value

var newFlagValue = 0;

for(var i = 0; i < lstFlags.length; i++) {

var checkBox = document.getElementById('cb' + i);

if(checkBox.checked) {

newFlagValue |= lstFlags[i][1];

}

}

var textbox = document.getElementById('tb');

textbox.value = newFlagValue;

explainFlags();

}

This page requires JavaScript. Please enable it in your browser settings.

This utility explains SAM flags in plain English.

Flag:  

Explanation:

for(var i = 0; i < lstFlags.length; i++) {

document.write("   " +lstFlags[i][0] + "
");

}

  read paired   read mapped in proper pair   read unmapped   mate unmapped   read reverse strand   mate reverse strand   first in pair   second in pair   not primary alignment   read fails platform/vendor quality checks   read is PCR or optical duplicate

Summary: