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
A21 F99 I1 R1 19 55.7 1970560 92.7% 1826709 142.9

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% 130.4 / 29.1 49coding (40/1389 nt)narUnitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base . (5/5);  new base A (19/20);  total (24/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*NC_000913_3_pae_tpiA1,544,0220CA91.8% 148.9 / NA 49L13F (TTG→TTT) narUnitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base C (3/1);  new base A (21/24);  total (24/25)
Fisher's exact test for biased strand distribution p-value = 3.49e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCG‑C‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAA  >  NC_000913_3_pae_tpiA/1543878‑1544169
                                                                                                                                                  |||                                                                                                                                                  
aTTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCG‑A‑aaaa                                                                                                                                                 <  1:15509/149‑1 (MQ=255)
  tggcaTTAACGGTAACCGTGACGAATGGCATCGAGACACAGTAAGCAAGGAGTACAGGACTGACTGATGTCTTGAGATTTCTTGTAGCAATATGTTTTCTTTTATTTTACCAGATGGCCGG‑GTTTTCTGGTTTCCAGTCGCG‑A‑aaaaag                                                                                                                                               <  2:944979/145‑3 (MQ=255)
    agaTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGATCAATATGTTTTCTTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCCCG‑A‑aaaaagat                                                                                                                                             >  1:381081/1‑145 (MQ=255)
       ttAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAAc                                                                                                                                           <  1:14631/149‑1 (MQ=255)
            ggTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCG‑CAAAAAGATAACGACtc                                                                                                                                      >  1:938695/1‑148 (MQ=255)
                   gcgcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTtct                                                                                                                               <  1:625341/149‑1 (MQ=255)
                      cTAAATAGCATCCAAACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCAt                                                                                                                            <  1:280356/149‑1 (MQ=255)
                       tAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCCTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCAtt                                                                                                                           <  1:354768/149‑1 (MQ=255)
                               aTCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGGTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCACGTCGCGAC‑ACAAGATAACGACTATTTTTCTCATCTTGCAGTg                                                                                                                   >  2:410962/1‑149 (MQ=255)
                                    gACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGCAATTTC‑AGAGGCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCata                                                                                                              >  1:228054/1‑149 (MQ=255)
                                      cacaGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCCCGCGGCATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATAtt                                                                                                            <  1:187093/149‑1 (MQ=255)
                                       acaGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTg                                                                                                           >  2:333383/1‑149 (MQ=255)
                                       acaGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTg                                                                                                           >  1:411606/1‑149 (MQ=255)
                                          gAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTc                                                                                                        <  1:59742/149‑1 (MQ=255)
                                            aGGCAAGAAGTAGACAACTGACGTATATCCAGAGACTTCTTCGGGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGAGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCt                                                                                                      <  2:338137/149‑1 (MQ=255)
                                              gCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTca                                                                                                    >  1:744429/1‑149 (MQ=255)
                                              gCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGACGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTTTTCCTcc                                                                                                    >  1:227885/1‑148 (MQ=255)
                                                aagaagTAGACAACTGACTGATGTCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAC‑GACAGCGACGGACTACCGGTTTAATTTTGCAGTGCCATATTGTTCCTcaca                                                                                                  >  2:454523/1‑149 (MQ=255)
                                                aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTATCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTcaca                                                                                                  <  1:133142/149‑1 (MQ=255)
                                                aagaagTAGACAACTGACCGGTATCGAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTcaca                                                                                                  <  2:404055/149‑1 (MQ=255)
                                                 agaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACAt                                                                                                 <  1:460671/149‑1 (MQ=255)
                                                      tAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATTTTGTTCCTTACATGcaca                                                                                            >  1:311174/1‑149 (MQ=255)
                                                         aCAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTACTCACATGCACACAt                                                                                         >  2:507112/1‑149 (MQ=255)
                                                           aaCTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCAGTCTTGTTCCTCACATGcaacaattg                                                                                       >  2:58200/1‑142 (MQ=255)
                                                             agtgcgtatatCCAGAGAGTTCTACGAGCAATATGTTTTCCTTAATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTACAGACGAG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGt                                                                                     <  2:938695/142‑1 (MQ=255)
                                                               gacgtatatCCAGAGATTTCTTGCAGATATTTGTCTTCTTCTATTTTCCCAGACGCCCGG‑ATTTTCTGGTTTCCAGCCGCG‑CAAAAATATAACGACCATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCGCATGCAGACATTGGTaa                                                                                   <  2:611588/144‑1 (MQ=255)
                                                                  tgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCa                                                                                                                      >  2:264251/1‑111 (MQ=255)
                                                                  tgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCa                                                                                                                      <  1:264251/111‑1 (MQ=255)
                                                                        ccAGACATTTCTTCGAGCAATATGTTTTCCTTTAATTTAACAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa                                                                          <  2:277275/149‑1 (MQ=255)
                                                                         cAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGTTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAg                                                                         <  1:368116/149‑1 (MQ=255)
                                                                           gagaTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTc                                                                                                        <  2:216239/116‑1 (MQ=255)
                                                                           gagaTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTc                                                                                                        >  1:216239/1‑116 (MQ=255)
                                                                                 tcttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAaca                                                                 >  2:736930/1‑149 (MQ=255)
                                                                                         cAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTaa                                                         <  1:333383/149‑1 (MQ=255)
                                                                                                ttttCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCaa                                                  >  1:656127/1‑149 (MQ=255)
                                                                                                ttttCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAGGGCGCaa                                                  >  1:148402/1‑149 (MQ=255)
                                                                                                tttgCCCTTACTCTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAATGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCaa                                                  <  2:148402/149‑1 (MQ=255)
                                                                                                    ccTGTATATTCCCAGAAGGCCGG‑GTTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGc                                              <  2:431153/149‑1 (MQ=255)
                                                                                                     cTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGGGGTAAGGAGCAATTGca                                             >  2:394916/1‑148 (MQ=255)
                                                                                                      tttATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCG‑AAAAAAGATAACGACTATTTTTCTCTTTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa                                            >  2:1032/1‑149 (MQ=255)
                                                                                                                 aGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAAt                                 >  1:747032/1‑149 (MQ=255)
                                                                                                                       ccGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTaa                              >  2:901294/1‑146 (MQ=255)
                                                                                                                       ccGG‑ATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTaa                              <  1:901294/146‑1 (MQ=255)
                                                                                                                            aTTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGaa                       <  1:176117/149‑1 (MQ=255)
                                                                                                                                tCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTgg                   >  2:788271/1‑149 (MQ=255)
                                                                                                                                tCTGGTGTCCAGTCGCG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGAGATATTGCCAGTTATTAGAATTAAGGATGAATTgg                   <  2:950989/149‑1 (MQ=255)
                                                                                                                                tCTGATATCAAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGATCCTCACATGCACACATTGGTAATGAAAAAAATACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTgg                   <  2:215172/149‑1 (MQ=255)
                                                                                                                                     tttCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGaa              >  2:918012/1‑149 (MQ=255)
                                                                                                                                         cAGTCGCG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGc          >  1:451738/1‑149 (MQ=255)
                                                                                                                                             tcgcgaaaaaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGa       <  1:736930/142‑1 (MQ=255)
                                                                                                                                                  aaaaaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTTGGTGAAGTGCTGTTTGaa  >  2:65506/3‑149 (MQ=255)
                                                                                                                                                  |||                                                                                                                                                  
ATTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGG‑ATTTTCTGGTTTCCAGTCGCG‑C‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAA  >  NC_000913_3_pae_tpiA/1543878‑1544169

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