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 F107 I1 R1 19 39.5 1386814 92.9% 1288350 143.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_pae_tpiA 1,544,022 1 bp→AA coding (39/1389 nt) narU ← nitrate/nitrite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA1,544,0211.A79.6% 129.1 / 31.8 49coding (40/1389 nt)narUnitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base . (4/6);  new base A (20/19);  total (24/25)
Fisher's exact test for biased strand distribution p-value = 7.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.39e-01
*NC_000913_3_pae_tpiA1,544,0220CA100.0% 162.8 / NA 49L13F (TTG→TTT) narUnitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (24/25);  total (24/25)

AGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑C‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAA  >  NC_000913_3_pae_tpiA/1543882‑1544170
                                                                                                                                              |||                                                                                                                                                    
agaTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑A‑aaa‑aagat                                                                                                                                              >  1:286447/1‑145 (MQ=255)
  atgaaCGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATaa                                                                                                                                             <  2:379229/146‑1 (MQ=255)
         gTAACTGCGCTAAATAGCATCTAGACACAGAAGGCAAGTAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACttt                                                                                                                                      >  2:610177/1‑147 (MQ=255)
                cgcAAAACAGCATCCAGACACAGAAGGGAAGAAGTAGACAACTGACTTATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTtctc                                                                                                                               <  2:222128/149‑1 (MQ=255)
                     ataaGCATACAAAAAAAGAAGGAAAGAAGTAGACAACTGTCTTATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTAAAAAAAAAA‑AAA‑AAA‑AGATAACGACTATTTTTCTCAtttt                                                                                                                          <  2:373063/146‑1 (MQ=255)
                     aaTAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACACCTATTTTTCTCAtttt                                                                                                                          >  2:507307/1‑149 (MQ=255)
                       tAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCACTCGC‑G‑AAAAA‑AGATAACGACTATTTTTCTCATTTTGc                                                                                                                        >  1:641074/1‑149 (MQ=255)
                        agcagcCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCa                                                                                                                       <  2:126998/149‑1 (MQ=255)
                         gCAGCCAGACACAGAAGGCAAGAAGTAGACAACTGATTTATATCGTGAGTTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTCCCAGTCGC‑G‑AAAAA‑AGATAACGACTATTTTTCTCATTTTGCAg                                                                                                                      <  1:208890/149‑1 (MQ=255)
                           aTCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCCTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAAAA‑AGATAACGACTATTTTTCTCATTTTGCAGTg                                                                                                                    <  1:123306/149‑1 (MQ=255)
                             ccAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGcc                                                                                                                  >  1:182502/1‑149 (MQ=255)
                              cAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGCCTATTTTTCTCATTTTGCGGTGCCa                                                                                                                 >  1:667053/1‑149 (MQ=255)
                                      gAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTc                                                                                                         >  1:168771/1‑149 (MQ=255)
                                      gAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTc                                                                                                         <  1:468243/149‑1 (MQ=255)
                                            aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTTTCATTTTTCAGTGCAATATTGTTTCTcaca                                                                                                   >  2:213636/1‑149 (MQ=255)
                                            aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTCTCCAGTCGC‑G‑A‑AAATAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTcaca                                                                                                   <  1:608832/149‑1 (MQ=255)
                                                 gTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGcac                                                                                              >  1:558297/1‑149 (MQ=255)
                                                 gTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGACAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGcac                                                                                              <  2:526970/149‑1 (MQ=255)
                                                  tAGACAACTGACTGATATACAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGTATTTTATGGATTACAATAACAA‑A‑AAA‑AGATAACGACTATTTTTCTCATTTTACAGTGCCATATTGTTCCTCACATGcgca                                                                                             >  1:244094/1‑149 (MQ=255)
                                                       aaCTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTg                                                                                        <  1:579112/149‑1 (MQ=255)
                                                            acttaTAGCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAAt                                                                                   <  2:242673/149‑1 (MQ=255)
                                                            actgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAAt                                                                                   >  1:128229/1‑149 (MQ=255)
                                                              tgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGa                                                                                 >  1:693001/1‑149 (MQ=255)
                                                              tgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCAACTGCACACCTTGGTAATGa                                                                                 >  2:674233/1‑149 (MQ=255)
                                                               gaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATCTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaa                                                                                <  1:231293/149‑1 (MQ=255)
                                                                atatCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTTCAGTGCCATATTGTTCCTCACATGCCCCCATTGCTAATCaaa                                                                               >  2:419240/1‑149 (MQ=255)
                                                                atatCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaa                                                                               <  1:534915/149‑1 (MQ=255)
                                                                    ccAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTGGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACCCATTGGTAATGaacaaaa                                                                           >  1:285539/1‑149 (MQ=255)
                                                                    ccAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa                                                                           <  1:525665/149‑1 (MQ=255)
                                                                    ccAGAGACTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa                                                                           <  1:150857/149‑1 (MQ=255)
                                                                      agagATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGa                                                                         <  2:182502/149‑1 (MQ=255)
                                                                           tttCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaaac                                                                    <  1:349509/149‑2 (MQ=255)
                                                                               ttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCGCAGTTGGGCGTGACATGCACACTTGGTTAATGAAAAACAGACAAAGCACg                                                                >  1:506690/1‑149 (MQ=255)
                                                                               ttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCCCGTGCACACATTGGTAATGAAAAAAAGACAAAACACg                                                                >  1:365407/1‑149 (MQ=255)
                                                                                tcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGa                                                               <  1:316107/149‑1 (MQ=255)
                                                                                         ctGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa                                                                           >  2:467136/2‑128 (MQ=255)
                                                                                         atGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa                                                                           <  1:467136/128‑1 (MQ=255)
                                                                                            ttttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCAt                                                                                                                             <  1:124900/75‑1 (MQ=255)
                                                                                            ttttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCAt                                                                                                                             >  2:124900/1‑75 (MQ=255)
                                                                                                 cTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAAAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGcc                                              <  2:558297/149‑1 (MQ=255)
                                                                                                  tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa                                             >  2:1765/1‑149 (MQ=255)
                                                                                                   ttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAg                                            <  1:443958/149‑1 (MQ=255)
                                                                                                         tCCCAGAAGGCCTGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGttatta                                      <  2:469648/149‑1 (MQ=255)
                                                                                                            cAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGaa                                   >  2:485550/1‑149 (MQ=255)
                                                                                                                   ccGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAAAACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGa                            >  2:11963/1‑149 (MQ=255)
                                                                                                                    cGGATTTTCTGGTTTCCAGTCGC‑G‑AAAAA‑AGATAACGACTATTTTTCTCATTTTGAAGTGCCATATTGGTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAAAACCCAGTTATTGCAACTAAGGAt                           >  2:667241/1‑149 (MQ=255)
                                                                                                                         tttCTGGTTGCCAGTCGC‑G‑AAAAA‑AGATACCGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAAtt                      <  1:507307/149‑1 (MQ=255)
                                                                                                                           tCTGGGTTCCAATTGC‑G‑AAAAA‑AGATAACGACTATTGTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTgg                    <  2:402341/149‑1 (MQ=255)
                                                                                                                                 ttCCAGTCGC‑GAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAg              >  1:521408/1‑149 (MQ=255)
                                                                                                                                         cggcgaaaaa‑aGAGAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGa        <  2:274095/142‑1 (MQ=255)
                                                                                                                                               aaaa‑aGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaaa  <  1:301660/148‑1 (MQ=255)
                                                                                                                                              |||                                                                                                                                                    
AGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑C‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAA  >  NC_000913_3_pae_tpiA/1543882‑1544170

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