454 Sequencing System “Universal” Accession Numbers

2. Data Files and Formats : 2.3 Standard File Formats : 2.3.7 454 Sequencing System “Universal” Accession Numbers

2.3.7

454 Sequencing System “Universal” Accession Numbers

The standard 454 read identifiers, used in 454 Sequencing System data analysis software versions prior to 1.0.52 (early GS 20 System), have the format “rank_x_y” (as in 003048_1034_0651), where “rank” is a ranking of the well in a region by signal intensity, and “x” and “y” are the pixel location of the well’s center on the sequencing Run images. This identifier is guaranteed to be unique only within the context of a single sequencing Run, and may or may not be unique across specific sets of Runs.

To allow for the combination of reads across larger data sets, a more unique accession number format has been developed. An accession in this format is a 14 character string, as in C3U5GWL01CBXT2, and consist of 4 components:

	C3U5GW	- a six character encoding of the timestamp of the Run
	L	- a randomizing “hash” character to enhance uniqueness
	01	- the region the read came from, as a two-digit number
	CBXT2	- a five character encoding of the X,Y location of the well

The timestamp, hash character and X,Y location use a base-36 encoding (where values 0-25 are the letters ‘A’-‘Z’ and the values 26-35 are the digits ‘0’-‘9’). An accession thus consists only of letters and digits, and is case-insensitive.

•	The timestamp is encoded by computing a “total” value as shown below, then converting it into a base-36 string:

(year - 2000) * 13 * 32 * 24 * 60 * 60 +

month * 32 * 24 * 60 * 60 +

day * 24 * 60 * 60 +

hour * 60 * 60 +

As a result of this calculation, the first character of read accessions will always be a letter for Runs performed from now until 2038. The timestamp values are taken from the rigRunName found in the analysisParms.parse file in the specified analysis directory. This rigRunName is the R_... name that is generated by the instrument software, and is also used as the standard directory name for the Run. Thus, a Run whose name begins with R_2004_09_22_16_59_10_... generates C3U5GW as its encoded timestamp value.

•	Since two Runs may be started at the same second, an additional base-36 character is generated by hashing the full rigRunName to a base-31 number (the highest prime below 36), as in:

chval = 0;

for (s=rigRunName; *s; s++) {

chval += (int) *s;

chval %= 31;

ch = (chval < 26 ? 'A' + chval : '0' + chval - 26);

•	The X,Y location is encoded by computing a total value of “X * 4096 + Y” and encoding that as a five character, base-36 string.