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 834,689 C→T 25.7% H1049H (CAC→CAT)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE834,6890CT25.7% 174.9 / 62.1 105H1049H (CAC→CAT) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (34/44);  new base T (17/10);  total (51/54)
Fisher's exact test for biased strand distribution p-value = 1.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.82e-01

Only 100 of 117 total aligned reads displayed.

TTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCGACACCCGTTCGGTGAA  >  minE/834620‑834757
                                                                     |                                                                    
ttACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAcc                                                                     <  1:1293817/71‑1 (MQ=255)
ttACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAcc                                                                     <  1:3237351/71‑1 (MQ=255)
 tACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                                                      >  1:2056047/1‑69 (MQ=255)
 tACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                                                      >  1:906431/1‑69 (MQ=255)
 tACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                                                      >  1:3263366/1‑69 (MQ=255)
 tACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                                                      >  1:3780668/1‑69 (MQ=255)
  acacCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAg                                                                   >  1:1594438/1‑71 (MQ=255)
  acacCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAg                                                                   >  1:3413186/1‑71 (MQ=255)
    acCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg                                                                 >  1:5194684/1‑71 (MQ=255)
    acCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg                                                                 <  1:1309397/71‑1 (MQ=255)
     ccAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg                                                                 <  1:3916310/70‑1 (MQ=255)
      cAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTgg                                                                >  1:4225396/1‑70 (MQ=255)
      cAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTgg                                                                >  1:1090091/1‑70 (MQ=255)
      cAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGa                                                               >  1:2432151/1‑71 (MQ=255)
        aCGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg                                                                 >  1:4478099/1‑67 (MQ=255)
        aCGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg                                                                 >  1:2991026/1‑67 (MQ=255)
        aCGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGTAACTGTATCAGGATCACCAg                                                                   <  1:325491/65‑1 (MQ=255)
        aCGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGTAACTGTATCAGGATCACCAg                                                                   <  1:872409/65‑1 (MQ=255)
        aCGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATg                                                             >  1:2006238/1‑71 (MQ=255)
         cGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGc                                                            <  1:948531/71‑1 (MQ=255)
         cGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGc                                                            <  1:3842395/71‑1 (MQ=255)
           ttCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTg                                                                 <  1:1613692/64‑1 (MQ=255)
            tCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGTg                                                         >  1:3554688/1‑71 (MQ=255)
             cACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCa                                                                    >  1:4803355/1‑59 (MQ=255)
                gAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGAttt                                                     >  1:2426852/1‑71 (MQ=255)
                gAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGAttt                                                     <  1:4714232/71‑1 (MQ=255)
                  gCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCg                                                   >  1:3534533/1‑71 (MQ=255)
                  gCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCg                                                   <  1:2854667/71‑1 (MQ=255)
                      aTCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGa                                               <  1:3230051/71‑1 (MQ=255)
                        cccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAcc                                                                     >  1:5323161/1‑47 (MQ=255)
                        cccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAcc                                                                     >  1:581817/1‑47 (MQ=255)
                        cccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTg                                                >  1:5589866/1‑68 (MQ=255)
                        cccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGa                                               >  1:3302829/1‑69 (MQ=255)
                        cccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGa                                               >  1:1361191/1‑69 (MQ=255)
                        cccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTCATTTCGGTGa                                               >  1:4694891/1‑69 (MQ=255)
                         ccgtGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGaaa                                             <  1:5323375/67‑1 (MQ=255)
                         ccgtGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAg                                            >  1:214927/4‑71 (MQ=255)
                         ccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGaaa                                             <  1:212152/70‑1 (MQ=255)
                         ccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGaaa                                             <  1:275250/70‑1 (MQ=255)
                          cATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGa                                               <  1:4888609/67‑1 (MQ=255)
                            tGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGCct                                         <  1:701343/71‑1 (MQ=255)
                            tGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGAGGCGTGCTTTTGGTGAAAGCct                                         <  1:1222393/71‑1 (MQ=255)
                              gCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCctgc                                       <  1:4569211/71‑1 (MQ=255)
                              gCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCctgc                                       <  1:3837109/71‑1 (MQ=255)
                               cGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCctgct                                      >  1:3832964/1‑71 (MQ=255)
                                gTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCa                                                                    >  1:1814474/1‑40 (MQ=255)
                                gTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCa                                                                    >  1:4693818/1‑40 (MQ=255)
                                 tACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                                                      <  1:181024/37‑1 (MQ=255)
                                 tACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                                                      <  1:5384262/37‑1 (MQ=255)
                                 tACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                                                      <  1:4558929/37‑1 (MQ=255)
                                 tACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                                                      <  1:424938/37‑1 (MQ=255)
                                   cGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGt                                   <  1:5029826/70‑1 (MQ=255)
                                    gCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGc                                           >  1:1064415/1‑61 (MQ=255)
                                    gCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGc                                           >  1:274199/1‑61 (MQ=255)
                                     ctctctGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTa                                <  1:2709479/71‑1 (MQ=255)
                                        tctGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCg                             >  1:4249911/1‑71 (MQ=255)
                                           ggTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTg                                                <  1:5050167/49‑1 (MQ=255)
                                           ggTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTg                                                <  1:5370868/49‑1 (MQ=255)
                                           ggTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTg                                                <  1:407910/49‑1 (MQ=255)
                                               gtcAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTccgccg                      <  1:4491433/71‑1 (MQ=255)
                                               gccagcagCTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGCCTGGTGGctt                                 <  1:3311403/58‑1 (MQ=255)
                                                tcAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAg                                            <  1:4158301/48‑1 (MQ=255)
                                                tcAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAg                                            <  1:2888177/48‑1 (MQ=255)
                                                tcAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAg                                            <  1:597352/48‑1 (MQ=255)
                                                tcAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTccgcc                       <  1:5683528/69‑1 (MQ=255)
                                                 cAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGt                                                 >  1:5359591/1‑42 (MQ=255)
                                                 cAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGt                                                 >  1:3626486/1‑42 (MQ=255)
                                                  agcagcTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGCCTGGTGGCTTATCGCCCGCCTATc                   <  1:2868745/71‑1 (MQ=255)
                                                  agcagcTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGCCTGGTGGCTTATCGCCCGCCTATc                   <  1:136506/71‑1 (MQ=255)
                                                  aGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTAt                               >  1:1661191/1‑59 (MQ=255)
                                                  aGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGt                            >  1:5052966/1‑62 (MQ=255)
                                                  aGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGa                     >  1:3815079/1‑69 (MQ=255)
                                                  aGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGa                     >  1:3327716/1‑69 (MQ=255)
                                                  aGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGa                     >  1:1724886/1‑69 (MQ=255)
                                                  aGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGAt                    >  1:154109/1‑70 (MQ=255)
                                                  aGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGAt                    >  1:2261944/1‑70 (MQ=255)
                                                  aGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATc                   <  1:247980/71‑1 (MQ=255)
                                                  aGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATc                   >  1:2032962/1‑71 (MQ=255)
                                                  aGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATc                   <  1:5529276/71‑1 (MQ=255)
                                                  aGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATc                   <  1:4205993/71‑1 (MQ=255)
                                                   gCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCg                  <  1:4420269/71‑1 (MQ=255)
                                                    cAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCg                  <  1:837594/70‑1 (MQ=255)
                                                    cAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCGa                 <  1:4825885/71‑1 (MQ=255)
                                                      aCTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCGaca               >  1:4505128/1‑71 (MQ=255)
                                                         ctATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGCCTGGTGGCTTATCGCCCGCCTATCGACAccc            >  1:3472373/2‑71 (MQ=255)
                                                         ctATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGCCTGGTGGCTTATCGCCCGCCTATCGACAcc             >  1:3260613/2‑70 (MQ=255)
                                                          tATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGa                     <  1:2438894/61‑1 (MQ=255)
                                                            tCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGCCTGGTGGCTTATCGCCCGCCTAt                    >  1:1388478/1‑60 (MQ=255)
                                                             cAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGCCTGGTGGCTTATCg                             >  1:724260/1‑50 (MQ=255)
                                                             cAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGCCTGGTGGCTTATCGCCCGCCTATCGACACCCGtag        >  1:557796/1‑69 (MQ=255)
                                                              aGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGCCTGGTGGCTTATCGCCCGCCTATCGACACCCGtagc       >  1:2117312/1‑68 (MQ=255)
                                                              aGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCGACACCCGTTCg       <  1:577294/71‑1 (MQ=255)
                                                              aGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCGACACCCGTTCg       <  1:334152/71‑1 (MQ=255)
                                                               ggATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCGac                <  1:12983/61‑1 (MQ=255)
                                                                gATCATCCGTGGATGCGTGCTTTTGGTGAAAGCCtggtgg                                    >  1:1901660/1‑40 (MQ=19)
                                                                gATCATCCGTGGATGCGTGCTTTTGGTGAAAGCCTGGTGGCATATcgcccgcc                       <  1:898825/53‑1 (MQ=255)
                                                                gATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCGACACCCGTTCGGt     <  1:3629170/71‑1 (MQ=255)
                                                                  tCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCGACACCCGTTCGGTGa   <  1:1917789/71‑1 (MQ=255)
                                                                  tCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCGACACCCGTTCGGTGa   <  1:3104137/71‑1 (MQ=255)
                                                                    aCCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCGACACCCGTTCGGTGaa  <  1:3637375/70‑1 (MQ=255)
                                                                     |                                                                    
TTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCGACACCCGTTCGGTGAA  >  minE/834620‑834757

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A