Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A23 F110 I0 R1 17 6.1 129814 98.7% 128126 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,343,438 C→T 100% intergenic (+114/+250) USA300HOU_RS11955 → / ← aldC_1 65 kDa membrane protein/Alpha‑acetolactate decarboxylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,343,4380CT100.0% 17.3 / NA 6intergenic (+114/+250)USA300HOU_RS11955/aldC_165 kDa membrane protein/Alpha‑acetolactate decarboxylase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (3/3);  total (3/3)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTA  >  USA300TCH1516_ALE/2343305‑2343558
                                                                                                                                     |                                                                                                                        
tACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTTTAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTa                                                                                                                   >  1:50605/1‑141 (MQ=255)
              aaaTAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAgt                                                                                                     <  1:25569/141‑1 (MQ=255)
                                                        aaTTGGCGTCGGTCTCTTTAGAAATTCACCTTATAAATCAAACTTGCTTGCTCCTAGTAGTACCAGATGGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAGCATAACAGCAGATCTCaa                                                           >  2:12493/1‑141 (MQ=255)
                                                                 ttGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGa                                                  <  2:15005/141‑1 (MQ=255)
                                                                                           aaTTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCt                        <  1:7842/141‑1 (MQ=255)
                                                                                                                 tagtaACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAAGATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGAtttatttta  >  1:1146/1‑141 (MQ=255)
                                                                                                                                     |                                                                                                                        
TACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTA  >  USA300TCH1516_ALE/2343305‑2343558

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A