Illumina qseq file format

Each record is one line with tab separator in the following format:

• Machine name: unique identifier of the sequencer.
• Run number: unique number to identify the run on the sequencer.
• Lane number: positive integer (currently 1-8).
• Tile number: positive integer.
• X: x coordinate of the spot. Integer (can be negative).
• Y: y coordinate of the spot. Integer (can be negative).
• Index: positive integer. No indexing should have a value of 1.
• Read Number: 1 for single reads; 1 or 2 for paired ends.
• Sequence (BASES)
• Quality: the calibrated quality string. (QUALITIES)
• Filter: Did the read pass filtering? 0 - No, 1 - Yes.

For more information, please refer to page 6 of: ftp://ftp.era.ebi.ac.uk/meta/doc/sra_1_1/SRA_File_Formats_Guide.pdf