Runs > Galaxy - DNAseq SNP > ReadsStats

Analysis ReadsStats

Statistics on reads and their qualities.
All data related to this analysis use 0. Bytes on the hard drive.
The analysis data has been purged on Wednesday 31st of July 2019.
Samples (6) Per position statistics Per sequence statistics
Quality N content Per base content Number of sequences Quality GC% Length Distribution Duplication Levels Kmer profiles Overrepresented sequences Adapter Content
SRR1425152-chr25_1 FAIL WARN PASS 2 287 270 PASS 48(WARN) 30-100(WARN) PASS FAIL PASS PASS
SRR1425152-chr25_2 PASS PASS PASS 2 287 270 PASS 48(WARN) 30-100(WARN) PASS FAIL PASS PASS
SRR1425153-chr25_1 PASS PASS PASS 4 073 864 PASS 48(FAIL) 30-100(WARN) PASS WARN PASS PASS
SRR1425153-chr25_2 PASS PASS PASS 4 073 864 PASS 48(FAIL) 30-100(WARN) PASS WARN PASS PASS
SRR1425154-chr25_1 PASS PASS PASS 4 064 564 PASS 48(FAIL) 30-100(WARN) PASS PASS PASS
SRR1425154-chr25_2 PASS PASS WARN 4 064 564 PASS 48(FAIL) 30-100(WARN) PASS WARN PASS PASS
All metrics :
With selection :

Help for per position statistics :

  • Quality : WARN = A warning will be issued if the lower quartile for any base is less than 10, or if the median for any base is less than 25. FAIL = This module will raise a failure if the lower quartile for any base is less than 5 or if the median for any base is less than 20.
  • GC% : WARN = This module issues a warning it the GC content of any base strays more than 5% from the mean GC content. FAIL = This module will fail if the GC content of any base strays more than 10% from the mean GC content.
  • N content : This module raises a warning if any position shows an N content of >5%. FAIL = This module will raise an error if any position shows an N content of >20%.
  • Per base content : WARN = This module issues a warning if the difference between A and T, or G and C is greater than 10% in any position. FAIL = This module will fail if the difference between A and T, or G and C is greater than 20% in any position.

Help for per sequence statistics :

  • Quality : WARN = A warning is raised if the most frequently observed mean quality is below 27 - this equates to a 0.2% error rate. FAIL = An error is raised if the most frequently observed mean quality is below 20 - this equates to a 1% error rate.
  • GC% : WARN = A warning is raised if the sum of the deviations from the normal distribution represents more than 15% of the reads. FAIL = This module will indicate a failure if the sum of the deviations from the normal distribution represents more than 30% of the reads.
  • Length distribution : WARN = This module will raise a warning if all sequences are not the same length. FAIL = This module will raise an error if any of the sequences have zero length.
  • Duplication level : WARN = This module will issue a warning if non-unique sequences make up more than 20% of the total. FAIL = This module will issue a error if non-unique sequences make up more than 50% of the total.
  • Kmer profiles : WARN = This module will issue a warning if any k-mer is enriched more than 3 fold overall, or more than 5 fold at any individual position. FAIL = This module will issue a error if any k-mer is enriched more than 10 fold at any individual base position.
  • Overrepresented sequences : WARN = This module will issue a warning if any sequence is found to represent more than 0.1% of the total. FAIL = This module will issue an error if any sequence is found to represent more than 1% of the total.
  • Disable grouping of bases for reads >50bp (--nogroup).
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