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
A1 F1 I2 R1 65 21.2 1002576 96.5% 967485 111.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 700,790 C→T A269T (GCT→ACT)  nagC ← N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913700,7900CT100.0% 33.0 / NA 11A269T (GCT→ACT) nagCN‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (5/6);  total (5/6)

GATGGTGCAGTCGTCCAGCGGCACGCGGCTCTGGTAGCCCTGCTTTAACAGATTCAACACCCGTTGTTCAATGGCAGCGTTGGCAGCGATAGTTTCCAGGCAGCCAAAGTTGCCGCAGTGGCAGCGTTCACCCAGCGGTTCGACCTGAATATGGCCAATTTCACCGACGTTGCCGTTGCGGCCAATAAAAATGCGCCCGTTAGAGATAATCCCGGC  >  NC_000913/700704‑700919
                                                                                      |                                                                                                                                 
gATGGTGCAGTCGTCCAGCGGCACGCGGCTCTGGTAGCCCTGCTTTAACAGATTCAACACCCGTTGTTCAATGGCAGCGTTGGCAGTGATAGTTTCCAGGCAGCCAAAGTTGCCGCAGTGGCAGCGTTCACCCAGCGGt                                                                               <  2:58625/139‑1 (MQ=255)
 aTGGTGCAGTCGTCCAGCGGCACGCGGCTCTGGTAGCCCTGCTTTAACAGATTCAACACCCGATGTTCAATGGCAGCGTTGGCAGTGATAGTTTCCAGGCAGCCAAAGTTGCCGCAGTGGCAGCGTTCACCCAGCGGtt                                                                              <  1:87733/139‑1 (MQ=255)
     tGCAGTCGTCCAGCGGCACGCGGCTCTGGTAGCCCTGCTTTAACAGATTCAACACCCGTTGTTCAATGGCAGCGTTGGCAGTGATAGTTTCCAGGCAGCCAAAGTTGCCGCAGTGGCAGCGTTCACCCAGCGGTTCGAc                                                                          <  1:405591/139‑1 (MQ=255)
               cAGCGGCACGCGGCTCTGGTAGCCCTGCTTTAACAGATTCAACACCCGTTGTTCAATGGCAGCGTTGGCAGTGATAGTTTCCAGGCAGCCAAAGTTGc                                                                                                         <  1:219828/98‑1 (MQ=255)
               cAGCGGCACGCGGCTCTGGTAGCCCTGCTTTAACAGATTCAACACCCGTTGTTCAATGGCAGCGTTGGCAGTGATAGTTTCCAGGCAGCCAAAGTTGc                                                                                                         >  2:219828/1‑98 (MQ=255)
                                           tttAACAGATTCAACACCCGTTGTTCAATGGCAGCGTTGGCAGTGATAGTTTCCAGGCAGCCAAAGTTGCCGCAGTGGCAGCGTTCACCCAGCGGTTCGACCTGAATATGGCCAATTTCACCGACGTTGCCGTTGCGGc                                    >  2:356627/1‑139 (MQ=255)
                                                              gttgttCAATGGCAGCGTTGGCAGTGATAGTTTCCAGGCAGCCAAAGTTGCCGCAGTGGCAGCGTTCACCCAGCGGTTCGACCTGAATATGGCCAATTTCACCGACGTTGCCGTTGCg                                      <  1:467705/118‑1 (MQ=255)
                                                              gttgttCAATGGCAGCGTTGGCAGTGATAGTTTCCAGGCAGCCAAAGTTGCCGCAGTGGCAGCGTTCACCCAGCGGTTCGACCTGAATATGGCCAATTTCACCGACGTTGCCGTTGCg                                      >  2:467705/1‑118 (MQ=255)
                                                              gttgttCAATGGCAGCGTTGGCAGTGATAGTTTCCAGGCAGCCAAAGTTGCCGCAGTGGCAGCGTTCACCCAGCGGTTCGACCTGAATATGGCCAATTTCACCGACGTTGCCGTTGCGGCCAATAAAAATGCGCCCGtt                 <  1:356627/139‑1 (MQ=255)
                                                                            gCGTTGGCAGTGATAGTTTCCAGGCAGCCAAAGTTGCCGCAGTGGCAGCGTTCACCCAGCGGTTCGACCTGAATATGGCCAATTTCACCGACGTTGCCGTTGCGGCCAATAAAAATGCGCCCGTTAGAGATAATCCCgg   >  2:224047/1‑139 (MQ=255)
                                                                             cGTTGGCAGTGATAGTTTCCAGGCAGCCAAAGTTGCCGCAGTGGCAGCGTTCACCCAGCGGTTCGACCTGAATATGGCCAATTTCACCGACGTTGCCGTTGCGGCCAATAAAAATGCGCCCGTTAGAGATAATCCCGGc  >  1:470811/1‑139 (MQ=255)
                                                                                      |                                                                                                                                 
GATGGTGCAGTCGTCCAGCGGCACGCGGCTCTGGTAGCCCTGCTTTAACAGATTCAACACCCGTTGTTCAATGGCAGCGTTGGCAGCGATAGTTTCCAGGCAGCCAAAGTTGCCGCAGTGGCAGCGTTCACCCAGCGGTTCGACCTGAATATGGCCAATTTCACCGACGTTGCCGTTGCGGCCAATAAAAATGCGCCCGTTAGAGATAATCCCGGC  >  NC_000913/700704‑700919

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A