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
A17 F6 I1 R1 16 39.4 1365814 93.3% 1274304 143.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_pae_tpiA 1,544,022 C→A L13F (TTG→TTT)  narU ← nitrate/nitrite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA1,544,0220CA100.0% 98.8 / NA 33L13F (TTG→TTT) narUnitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (17/16);  total (17/16)

AGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑C‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTG  >  NC_000913_3_pae_tpiA/1543882‑1544155
                                                                                                                                              |                                                                                                                                       
agaTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTGGC‑G‑A‑aaaaagat                                                                                                                                >  1:641857/1‑145 (MQ=255)
 gaTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑A‑aaaaagata                                                                                                                               >  1:299288/1‑144 (MQ=255)
  aTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATaa                                                                                                                              <  1:570432/149‑1 (MQ=255)
        ggTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTAGC‑GAA‑AAAA‑GATAACGACTa                                                                                                                        >  2:636177/1‑149 (MQ=255)
                  cTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑A‑AAAACGATAACGACTATTTTTCTCAt                                                                                                              >  2:581250/1‑149 (MQ=255)
                          cATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGt                                                                                                      <  1:235285/149‑1 (MQ=255)
                            tCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTTCCGTGc                                                                                                    >  2:433071/1‑149 (MQ=255)
                               aGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATGTGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATaa                                                                                                                              <  1:36157/120‑1 (MQ=255)
                               aGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATaa                                                                                                                              >  2:36157/1‑120 (MQ=255)
                                      taaGTCAATAAGTAGACAACTTACTGATTTCCAGTGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTc                                                                                          <  2:646090/148‑1 (MQ=255)
                                         agcaaagagTAGAAAACTGACTGATATCCAGAGATTTCTTCGAGCCATAGGTTTTCCTTTATTTTCACAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAAAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTc                                                                                       <  2:116359/142‑1 (MQ=255)
                                           cAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGATGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAAAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTcac                                                                                     <  1:67258/149‑1 (MQ=255)
                                            aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTca                                                                                      >  1:473093/1‑147 (MQ=255)
                                            aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTca                                                                                      <  2:473093/147‑1 (MQ=255)
                                              gaagTAGACAACTGACTGATATCCATAGTTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATg                                                                                  <  1:186735/149‑1 (MQ=255)
                                                      cAACTGACTGATATCCAGAGATTTCTTCGAGCAATCTGTTTTCCTTTATTTTCACAGCAGCCAAGATATTCTGGTTTCTAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTGCTCTTTTTGCAGTACCATATTGTTCCTCACATGCACACAtt                                                                          >  2:504444/1‑149 (MQ=255)
                                                       aaCTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTg                                                                         >  2:204300/1‑149 (MQ=255)
                                                           gactgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTaa                                                                     >  2:289427/1‑149 (MQ=255)
                                                                          aTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGGCGCGG‑A‑AAAA‑GATAACGACTATTTTTCTCATTTTTCAGTGCCTTATTGTTCCTCACATGCACACATTGGTATTGGAAAAAAAACaaa                                                      >  1:197946/1‑149 (MQ=255)
                                                                          aTTTCTTCGAGCAATATGTTTTCCATTATTTTCCCAGAATGCCGTATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATGTTATTCCTCACATGAACCCATTGGTAATAAAAAAAAGACaaa                                                      >  2:289844/1‑149 (MQ=255)
                                                                           tttCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaaaa                                                     >  1:277544/1‑149 (MQ=255)
                                                                           tttCTTCGAGCAATATGTTTTCCTATATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaaaa                                                     <  1:584662/149‑1 (MQ=255)
                                                                            ttcttcGAGCAATATGTTTTCCTTTATTTTCCCAGACGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGCCTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAac                                                    <  1:285714/149‑1 (MQ=255)
                                                                                   aGCAATATGTTTTCTTTTAATTAAACAGAAGGCCGGATTTTCTGGGTTCAAGTCGC‑G‑AAAAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACAAAAAAAAAAAAAAAAAAAGACAAAACACGAGGt                                             <  2:277544/149‑1 (MQ=255)
                                                                                      aaTATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAg                                          <  1:289427/149‑1 (MQ=255)
                                                                                          ggTTTTCCATTATTTGCCTGAAACGCCGGATTTTTTGGTTTCCAGTCCC‑G‑AAAAAA‑GATAACGACTATTTTACTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGgcgc                                      <  2:406647/148‑1 (MQ=255)
                                                                                               tCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTGATGAAAAAAAGACAAAACACGAGGTAGGGCCCAATAg                                 >  2:17328/1‑149 (MQ=255)
                                                                                                cccttATTTCCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGc                                <  1:184275/146‑1 (MQ=255)
                                                                                                                   ccGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTcc                                                                                         <  2:213475/73‑1 (MQ=255)
                                                                                                                   ccGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTcc                                                                                         >  1:213475/1‑73 (MQ=255)
                                                                                                                          ttCTGGTTTCCAGTCGC‑G‑AAAAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTg      >  2:450118/1‑149 (MQ=255)
                                                                                                                             tGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGt   >  1:376684/1‑149 (MQ=255)
                                                                                                                              ggTTGCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTg  <  1:5125/149‑1 (MQ=255)
                                                                                                                                              |                                                                                                                                       
AGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑C‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTG  >  NC_000913_3_pae_tpiA/1543882‑1544155

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A