Basic Statistics

Summary

The Basic Statistics module generates some simple composition statistics for the file analysed.

• File Name：The original filename of the file which was analysed
• File type：Says whether the file appeared to contain actual base calls or colorspace data which had to be converted to base calls
• Phred Encoding：Says which ASCII encoding of quality values was found in this file.
• Total Reads：A count of the total number of sequences processed.
• Total Bases：A count of the total number of bases in all sequences processed.
• Total T Bases：A count of the total number of base 'T' in all sequences processed.
• Total C Bases：A count of the total number of base 'C' in all sequences processed.
• Total G Bases：A count of the total number of base 'G' in all sequences processed.
• Total A Bases：A count of the total number of base 'A' in all sequences processed.
• Total N Bases： A count of the total number of base 'N' in all sequences processed , where 'N' is the base that cannot be recognized by sequencing.
• %GC：The overall %GC of all bases in all sequences
• Min Length：The length of the shortest sequence in the set.
• Max Length：The length of the highest sequence in the set.
• Lowest Char: The lowest quality char in all sequences processed.
• Highest Char: The highest quality char in all sequences processed.

Example

"basic_stats"：{
            "file_name"："test.fastq.gz",
            "file_type"："",
            "phred"：{
                "name"："Sanger / Illumina 1.9",
                "offset"：33
            },
            "total_reads"：250000,
            "total_bases"：37500000,
            "t_count"：8473918,
            "c_count"：10050719,
            "g_count"：9888266,
            "a_count"：9086549,
            "n_count"：548,
            "gc_percentage"：0.5317062666666666,
            "min_length"：150,
            "max_length"：150,
            "lowest_char"：35,
            "highest_char"：70
        },