# 详解Bowtie2的比对Summary

Bowtie的中文意思是：领结，蝴蝶结

Bowtie2是比对软件Bowtie的第二版本，主要改进了支持gap比对。

Bowtie2用户手册：

http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml 在看比对结果前需要了解三个概念：

1. Aligned concordantly 合理比对

2. Multiple alignments 多重比对

### Default mode: search for multiple alignments, report the best one, 也即是：多重比对，只取最好的那个alignment。

3. Bowtie2在双端比对下：

Alignment summary

# 单端比对：

For datasets consisting of unpaired reads, the summary might look like this:

20000 (100.00%) were unpaired; of these:

1247 (6.24%) aligned 0 times

18739 (93.69%) aligned exactly 1 time

14 (0.07%) aligned >1 times

93.77% overall alignment rate

# 翻译下即：

其中，

其中，

总共的比对率是：(18739+14)/20000=93.77%

# 双端比对：

For datasets consisting of pairs, the summary might look like this:

10000 (100.00%) were paired; of these:

650 (6.50%) aligned concordantly 0 times

8823 (88.23%) aligned concordantly exactly 1 time

527 (5.27%) aligned concordantly >1 times

----

650 pairs aligned concordantly 0 times; of these:

34 (5.23%) aligned discordantly 1 time

----

616 pairs aligned 0 times concordantly or discordantly; of these:

1232 mates make up the pairs; of these:

660 (53.57%) aligned 0 times

571 (46.35%) aligned exactly 1 time

1 (0.08%) aligned >1 times

96.70% overall alignment rate

# 翻译下即：

其中，

10000个pairs都是paired也即双端数据；

其中，

650个pairs没有合理比对上；

8823个pairs只合理比对上一次；

527个pairs合理比对多于一次；

在650个pairs没有合理比对上的pairs中：

34个pairs可以不合理比对上一次；

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