What is does

This tool creates summary statistics on a FASTQ file.

TIP: This statistics report can be used as input for the Boxplot tools.

The output file will contain the following fields:

• column = column number (1 to 36 for a 36-cycles read Solexa file)
• count = number of bases found in this column.
• min = Lowest quality score value found in this column.
• max = Highest quality score value found in this column.
• sum = Sum of quality score values for this column.
• mean = Mean quality score value for this column.
• Q1 = 1st quartile quality score.
• med = Median quality score.
• Q3 = 3rd quartile quality score.
• IQR = Inter-Quartile range (Q3-Q1).
• lW = 'Left-Whisker' value (for boxplotting).
• rW = 'Right-Whisker' value (for boxplotting).
• outliers = Scores falling beyond the left and right whiskers (comma separated list).
• A_Count = Count of 'A' nucleotides found in this column.
• C_Count = Count of 'C' nucleotides found in this column.
• G_Count = Count of 'G' nucleotides found in this column.
• T_Count = Count of 'T' nucleotides found in this column.
• N_Count = Count of 'N' nucleotides found in this column.
• Other_Nucs = Comma separated list of other nucleotides found in this column.
• Other_Count = Comma separated count of other nucleotides found in this column.

For example:

#column   count   min max sum mean    Q1  med Q3  IQR lW  rW  outliers    A_Count C_Count G_Count T_Count N_Count other_bases other_base_count
1   14336356    2   33  450600675   31.4306281875   32.0    33.0    33.0    1.0 31  33  2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30    4482314 2199633 4425957 3208745 19707
2   14336356    2   34  441135033   30.7703737965   30.0    33.0    33.0    3.0 26  34  2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25   4419184 2170537 4627987 3118567 81
3   14336356    2   34  433659182   30.2489127642   29.0    32.0    33.0    4.0 23  34  2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22    4310988 2941988 3437467 3645784 129
4   14336356    2   34  433635331   30.2472490917   29.0    32.0    33.0    4.0 23  34  2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22    4110637 3007028 3671749 3546839 103
5   14336356    2   34  432498583   30.167957813    29.0    32.0    33.0    4.0 23  34  2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22    4348275 2935903 3293025 3759029 124

Adapter bases in color space reads are excluded from statistics.