SAM是Sequence Alignment/Map 的縮寫。像bwa等軟件序列比對結果都會輸出這樣的文件。samtools網站上有專門的文檔介紹SAM文件。具體地址：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。根據文檔介紹我們可以計算，但是為了方便大家，下面給大家提供一個腳本工具，大家直接輸入flag值就可以知道它代表的含義了。

該腳本的使用方法如下截圖所示：

腳本工具的使用方法：

將下面的代碼保存在記事本里面，另存為一個html文件，如文件名：FlagExplain.html(拓展名一定要為.html)。雙擊既可以在瀏覽器里面打開了。

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: