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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 835,819 T→C 31.6% Y179Y (TAT→TAC)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,8190TC31.6% 116.2 / 78.0 98Y179Y (TAT→TAC) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base T (24/43);  new base C (22/9);  total (46/52)
Fisher's exact test for biased strand distribution p-value = 2.05e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 104 total aligned reads displayed.

AAAGACAAGAACTTCGACAACATCCAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGAT  >  minE/835751‑835884
                                                                    |                                                                  
aaaGACAAGAACTTCGACAACATCCAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTAttt                                                                  <  1:3531289/71‑1 (MQ=255)
aaaGACAAGAACTTCGACAACATCCAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTAttt                                                                  >  1:44376/1‑71 (MQ=255)
  aGACAAGAACTTCGACAACATCCAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGc                                                                >  1:4756403/1‑71 (MQ=255)
        caaCTTCGAGGCCATGCAAAAGGAGATGTACGGGCAGTTTGAAAACACCTTCATGATGTACCTGCCgcgc                                                           >  1:594367/2‑70 (MQ=255)
        caaCTTCGAGGCCATGCAAAAGGAGATGTACGGGCAGTTTGAAAACACCTTCATGATGTACCTGCCGCGcc                                                          >  1:3923764/2‑71 (MQ=255)
          aCTTCGACAACATCCAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTAt                                                                    >  1:125370/1‑59 (MQ=255)
          aCTTCGACAACATCCAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTAt                                                                    >  1:1884637/1‑59 (MQ=255)
           cTTCGACAACATCCAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCcgc                                                             <  1:4191217/65‑1 (MQ=255)
             tCGACAACATCCAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTAt                                                                    >  1:2531262/1‑56 (MQ=255)
             tCGACAACATCCAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCtgtg                                                      >  1:773307/1‑70 (MQ=255)
             tCGACAACATCCAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGc                                                     >  1:2789212/1‑71 (MQ=255)
              cGACAACATCCAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCgcgc                                                           <  1:3201256/64‑1 (MQ=255)
              cGACAACATCCAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGc                                                     >  1:631081/1‑70 (MQ=255)
                acaacaTCCAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGag                                                  <  1:686382/71‑2 (MQ=255)
                acaacaTCCAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGaa                                                  <  1:5528516/71‑1 (MQ=255)
                acaacaTCCAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGaa                                                  <  1:1707990/71‑1 (MQ=255)
                  aacaTCCAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAaca                                                <  1:4207407/71‑1 (MQ=255)
                        caaaaGGAGATGTACGGGCAGTTTGAAAACACCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCt                                          >  1:432562/4‑71 (MQ=255)
                        caaaaGGAGATGTACGGGCAGTTTGAAAACACCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCt                                          >  1:2853531/4‑71 (MQ=255)
                        cAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGcc                                           <  1:1291312/70‑1 (MQ=255)
                        cAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCt                                          >  1:5462064/1‑71 (MQ=255)
                        cAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCt                                          <  1:5149149/71‑1 (MQ=255)
                         aGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCt                                          >  1:4348567/1‑70 (MQ=255)
                         aGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTg                                         <  1:1781324/71‑1 (MQ=255)
                         aGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTg                                         <  1:3186099/71‑1 (MQ=255)
                         aGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTg                                         <  1:1663632/71‑1 (MQ=255)
                          aaaGGAGATGTACGGGCAGTTTGAAAACACCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCtca                                        <  1:3666103/70‑3 (MQ=255)
                            aGGAGATGTACGGGCAGTTTGAAAACACCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCaat                                      >  1:3079316/1‑70 (MQ=255)
                            aGGAGATGTACGGGCAGTTTGAAAACACCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCaat                                      >  1:3935238/1‑70 (MQ=255)
                              gagATGTACGGGCAGTTTGAAAACACCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCAA‑tcc                                   <  1:5372620/69‑1 (MQ=255)
                              gCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑ccc                                   <  1:560082/71‑1 (MQ=255)
                              gCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑cc                                    <  1:691822/70‑1 (MQ=255)
                               cGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCt                                          >  1:3961053/1‑64 (MQ=255)
                                gATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCtg                                                        >  1:2120516/1‑49 (MQ=255)
                                gATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCgg                                 <  1:5176742/71‑1 (MQ=255)
                                gATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCgg                                 <  1:2563743/71‑1 (MQ=255)
                                gATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCgg                                 <  1:5643594/71‑1 (MQ=255)
                                gATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCgg                                 <  1:1687524/71‑1 (MQ=255)
                                    tataGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCtg                                                        <  1:698975/45‑1 (MQ=255)
                                       aGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCAtgtgt                          >  1:1436486/1‑71 (MQ=255)
                                           aGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGc                       >  1:2746859/1‑70 (MQ=255)
                                            gTTTGAAAACACCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGa                     >  1:4997169/1‑71 (MQ=255)
                                            gTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCa                               <  1:2105302/61‑1 (MQ=255)
                                            gTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCa                               <  1:370947/61‑1 (MQ=255)
                                            gTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCg                      <  1:4811165/70‑1 (MQ=255)
                                            gTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCg                      <  1:4585217/70‑1 (MQ=255)
                                            gTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCg                      <  1:1012600/70‑1 (MQ=255)
                                             ttCGAAAACACCTTCATGATGTATTTGCCGCGCCtg                                                        <  1:1471726/36‑1 (MQ=255)
                                             ttCGAAAACACCTTCATGATGTATTTGCCGCGCCtg                                                        <  1:1620059/36‑1 (MQ=255)
                                             ttCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGc                                <  1:4370896/59‑1 (MQ=255)
                                              ttgAAAACAACTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGAcc                   >  1:3261578/3‑71 (MQ=255)
                                              tCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACt                                              >  1:2540103/1‑45 (MQ=255)
                                              tCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGaa                                       <  1:5537493/52‑1 (MQ=255)
                                              tCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGaa                                       <  1:3212023/52‑1 (MQ=255)
                                              tCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGaa                                       <  1:149834/52‑1 (MQ=255)
                                              tCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCAtgtg                           >  1:2505592/1‑63 (MQ=255)
                                               tgAAAACACCTTCATGATGTACCTGCCGCGCCTGTGCGCACACTGCCTCAATCCCAGC‑TGCGTGGCGACCt                  >  1:2191295/2‑71 (MQ=255)
                                               tgAAAACACCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCt                  >  1:664389/2‑71 (MQ=255)
                                               tgAAAACACCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCt                  >  1:727956/2‑71 (MQ=255)
                                               tgAAAACACCTTCATGATGTACATGCCGCGCCTGTGCGAACACTGCCTCaa                                       >  1:1353259/2‑51 (MQ=255)
                                               cGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCAtgtg                           >  1:5626662/1‑62 (MQ=255)
                                               cGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCAtgt                            <  1:2833587/61‑1 (MQ=255)
                                               cGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCt                  >  1:139118/1‑71 (MQ=255)
                                               cGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCt                  >  1:83831/1‑71 (MQ=255)
                                               cGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCt                  >  1:4604916/1‑71 (MQ=255)
                                                gAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑cc                                    >  1:4653343/1‑52 (MQ=255)
                                                gAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑cc                                    >  1:2313407/1‑52 (MQ=255)
                                                gAAAACACCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTTCCTCAATCCCAGC‑TGCGTGGCGACCTg                 >  1:2362692/1‑71 (MQ=255)
                                                gAAAACACCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTg                 >  1:4134574/1‑71 (MQ=255)
                                                 aaaaCACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGc                <  1:2847320/71‑1 (MQ=255)
                                                 aaaaCACCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGc                >  1:559860/1‑71 (MQ=255)
                                                  aaaCACCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCaa                                       >  1:1943985/1‑48 (MQ=38)
                                                  aaaCACCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCaa                                       >  1:5518181/1‑48 (MQ=38)
                                                   aaCACCTTCATGATGTATTTGCCGCGCCTCTGCGAACACTGCCt                                          >  1:4406981/1‑44 (MQ=255)
                                                    acacCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCg             <  1:3126183/71‑1 (MQ=255)
                                                    acacCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCg             <  1:1157043/71‑1 (MQ=255)
                                                    acacCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGccca             <  1:3838918/71‑2 (MQ=255)
                                                    acacCTTCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGccca             <  1:3879190/71‑2 (MQ=255)
                                                     cacCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGccc              >  1:2062836/1‑69 (MQ=255)
                                                      acCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAg           <  1:2239291/71‑1 (MQ=255)
                                                      acCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAg           <  1:1122157/71‑1 (MQ=255)
                                                      acCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAg           <  1:2812730/71‑1 (MQ=255)
                                                      acCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAg           <  1:3395560/71‑1 (MQ=255)
                                                       ccTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTg                                         <  1:1034980/41‑1 (MQ=255)
                                                       ccTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTg                                         <  1:5573785/41‑1 (MQ=255)
                                                       ccTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAg           <  1:5009832/70‑1 (MQ=255)
                                                       ccTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGc          >  1:1982968/1‑71 (MQ=255)
                                                          tCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGt       >  1:4422061/1‑71 (MQ=255)
                                                          tCATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCggc       >  1:1641382/1‑70 (MQ=255)
                                                           cATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCaa                                       >  1:3309811/1‑39 (MQ=25)
                                                           cATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCggc       <  1:4020327/70‑2 (MQ=255)
                                                           cATGATGTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCgg        <  1:860058/69‑1 (MQ=255)
                                                            atgatgTACCTGCCGCGCCTGTGCGAACACTGCCTCaa                                       >  1:2073067/1‑38 (MQ=25)
                                                            atgatgTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCgg        <  1:73443/68‑1 (MQ=255)
                                                            atgatgTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGgcgc     >  1:3207135/1‑71 (MQ=255)
                                                             tgatgTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGgcgct    <  1:5492776/71‑2 (MQ=255)
                                                             tgatgTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCACAGC‑TGCGTGGCGACCTGCCCAAGCGgcgc     >  1:3424952/1‑70 (MQ=255)
                                                               atgTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGAt  <  1:5454100/71‑1 (MQ=255)
                                                               atgTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGAt  <  1:4593942/71‑1 (MQ=255)
                                                               atgTACCTGCCGCGCCTGTGCGAACACTGCCTCAATCCCAGC‑TGCGTGGCGACCTGCCCAAGCGgcgcta   <  1:1889141/70‑3 (MQ=255)
                                                                    |                                                                  
AAAGACAAGAACTTCGACAACATCCAGAAGGCGATGTATAGCCAGTTCGAAAACACCTTCATGATGTATTTGCCGCGCCTGTGCGAACACTGCCTGAA‑CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGAT  >  minE/835751‑835884

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A