爲了便於測序數據的發佈和共享，高通量測序數據以FASTQ 格式來記錄所測的鹼基讀段和質量分數．如下圖 所示，FASTQ 格式以測序讀段爲單位存儲，每條讀段佔4 行，其中第1 行和第3行由文件識別標誌和讀段名(ID)組成(第1 行以“@”開頭而第3 行以“+”開頭；第3 行中ID 可以省略，但“+”不能省略)，第2 行爲鹼基序列，第4行爲對應的測序質量分數．
FastQ數據格式
1.序列名稱：
對於每一條FastQ序列，都有一個可以唯一標示的序列名稱，如下：
1 | @HWUSI-EAS100R:6:73:941:1973#0/1 |
| HWUSI-EAS100R | the unique instrument name |
|---|---|
| 6 | flowcell lane |
| 73 | tile number within the flowcell lane |
| 941 | 'x'-coordinate of the cluster within the tile |
| 1973 | 'y'-coordinate of the cluster within the tile |
| #0 | index number for a multiplexed sample (0 for no indexing) |
| /1 | the member of a pair, /1 or /2 (paired-end or mate-pair reads only) |
Versions of the Illumina pipeline since 1.4 appear to use #NNNNNN instead of #0 for the multiplex ID, where NNNNNN is the sequence of the multiplex tag.
With Casava 1.8 the format of the '@' line has changed:
1 | @EAS139:136:FC706VJ:2:2104:15343:197393
1:Y:18:ATCACG |
| EAS139 | the unique instrument name |
|---|---|
| 136 | the run id |
| FC706VJ | the flowcell id |
| 2 | flowcell lane |
| 2104 | tile number within the flowcell lane |
| 15343 | 'x'-coordinate of the cluster within the tile |
| 197393 | 'y'-coordinate of the cluster within the tile |
| 1 | the member of a pair, 1 or 2 (paired-end or mate-pair reads only) |
| Y | Y if the read fails filter (read is bad), N otherwise |
| 18 | 0 when none of the control bits are on, otherwise it is an even number |
| ATCACG | index sequence |
2、質量值：對於每一條序列，其每一個鹼基都有一個對應的測序質量值：
傳統測序的質量值是基於Phred quality scores，定義如下：
Phred quality scores Q are defined as a property which is logarithmically related to the base-calling error probabilities P.
Q=-10 log10P Phred quality scores are logarithmically linked to error probabilities
| Phred Quality Score | Probability of incorrect base call | Base call accuracy |
|---|---|---|
| 10 | 1 in 10 | 90 % |
| 20 | 1 in 100 | 99 % |
| 30 | 1 in 1000 | 99.9 % |
| 40 | 1 in 10000 | 99.99 % |
| 50 | 1 in 100000 | 99.999 % |
The Solexa pipeline (i.e., the software delivered with the Illumina Genome Analyzer) earlier used a different mapping, encoding the odds p/(1-p) instead of the probability p:
Although both mappings are asymptotically identical at higher quality values, they differ at lower quality levels (i.e., approximately p > 0.05, or equivalently, Q < 13).
爲了便於序列存儲，通常採用單字符來標示序列的質量值。至於序列的quality values值，是通過一些算法得出來的。即：用字母的ASCII值減去相應的數（不同測序平臺數值不一樣），然後就得到Q值，然後通過前面的計算公式計算出鹼基的測序錯誤率。
下面是不同測序平臺使用的字符區間段：
