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 834,659 C→G 21.4% L1039L (CTC→CTG)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE834,6590CG21.4% 249.9 / 63.6 126L1039L (CTC→CTG) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (43/56);  new base G (16/11);  total (59/67)
Fisher's exact test for biased strand distribution p-value = 1.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.84e-01

Only 100 of 134 total aligned reads displayed.

GAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTA  >  minE/834591‑834727
                                                                    |                                                                    
gAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctctc                                                                    >  1:5173350/1‑71 (MQ=255)
gAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctctc                                                                    <  1:1764458/71‑1 (MQ=255)
  aGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTg                                                                  <  1:1013436/71‑1 (MQ=255)
     tGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctcac                                                                    >  1:223304/1‑64 (MQ=255)
      gAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGgtcg                                                              >  1:1469327/1‑71 (MQ=255)
       aaCACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGgtcgt                                                             <  1:2843237/71‑1 (MQ=255)
        acacGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGgtcgt                                                             >  1:4333227/1‑70 (MQ=255)
          acGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAg                                                          >  1:1235246/1‑71 (MQ=255)
          acGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAg                                                          >  1:5009384/1‑71 (MQ=255)
              ttCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGc                                                         >  1:2621404/1‑68 (MQ=255)
              ttCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGc                                                         >  1:2614700/1‑68 (MQ=255)
              ttCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGc                                                         >  1:4392780/1‑68 (MQ=255)
               tCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACt                                                     >  1:1481969/1‑71 (MQ=255)
                cTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGgt                                                                >  1:3420004/1‑59 (MQ=255)
                 ttACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTg                                                                  >  1:2963754/1‑56 (MQ=255)
                 ttACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTg                                                                  >  1:863518/1‑56 (MQ=255)
                 ttACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTg                                                                  >  1:1440838/1‑56 (MQ=255)
                 ttACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTg                                                                  >  1:1369880/1‑56 (MQ=255)
                   ataaCGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTAt                                                 >  1:924770/3‑71 (MQ=255)
                    taaCGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATc                                                <  1:4506961/70‑1 (MQ=255)
                     aaCGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTAt                                                 >  1:3529316/1‑69 (MQ=255)
                     aaCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTAt                                                 >  1:3079501/1‑69 (MQ=255)
                     aaCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                                               <  1:1352667/71‑1 (MQ=255)
                     aaCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                                               <  1:5049300/71‑1 (MQ=255)
                     aaCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                                               <  1:615685/71‑1 (MQ=255)
                      aCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctc                                                                      <  1:4091012/47‑1 (MQ=255)
                      aCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctc                                                                      <  1:5262474/47‑1 (MQ=255)
                      aCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                                               <  1:5645872/70‑1 (MQ=255)
                             ttACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAg                                              <  1:2815240/64‑1 (MQ=255)
                             ttACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAcc                                       <  1:3237351/71‑1 (MQ=255)
                             atACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCatc                                       >  1:3748264/2‑69 (MQ=255)
                              tACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGa                                            <  1:4099391/65‑1 (MQ=255)
                              tACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCatcc                                      >  1:1238355/1‑68 (MQ=255)
                              tACACCAACGTTCACGAGCTGATCCCATGGCGTACGctc                                                                      >  1:4909502/1‑39 (MQ=255)
                              tACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                        >  1:3780668/1‑69 (MQ=255)
                              tACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                        >  1:3263366/1‑69 (MQ=255)
                               acacCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAg                                     >  1:3413186/1‑71 (MQ=255)
                               acacAAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAg                                     >  1:2207608/1‑71 (MQ=255)
                                cacCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGgtcgt                                                             <  1:876296/46‑1 (MQ=255)
                                cacCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGgtcgt                                                             <  1:3450753/46‑1 (MQ=255)
                                 acCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAg                                              <  1:3148503/60‑1 (MQ=255)
                                 acCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAg                                              <  1:5362383/60‑1 (MQ=255)
                                 acCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg                                   <  1:1309397/71‑1 (MQ=255)
                                 acCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGgtcgt                                                             <  1:2697382/45‑1 (MQ=255)
                                  ccAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg                                   <  1:3916310/70‑1 (MQ=255)
                                   cAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTgg                                  >  1:1090091/1‑70 (MQ=255)
                                   cAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGa                                 >  1:2432151/1‑71 (MQ=255)
                                   cAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGa                                 >  1:1345052/1‑71 (MQ=255)
                                     aCGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg                                   >  1:2991026/1‑67 (MQ=255)
                                     aCGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg                                   >  1:4638739/1‑67 (MQ=255)
                                     aCGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg                                   >  1:4478099/1‑67 (MQ=255)
                                     aCGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGTAACTGTATCAGGATCACCAg                                     <  1:872409/65‑1 (MQ=255)
                                     aCGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATg                               >  1:2006238/1‑71 (MQ=255)
                                      cGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGc                              <  1:3842395/71‑1 (MQ=255)
                                        ttCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGt                            >  1:1960647/1‑71 (MQ=255)
                                        ttCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                                               <  1:4081904/52‑1 (MQ=255)
                                        ttCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                                               <  1:3479341/52‑1 (MQ=255)
                                        ttCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                                               <  1:2628966/52‑1 (MQ=255)
                                        ttCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGAt                                           <  1:1430241/56‑1 (MQ=255)
                                        ttCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTg                                   <  1:1613692/64‑1 (MQ=255)
                                         tCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGTg                           >  1:3554688/1‑71 (MQ=255)
                                          cACGAGCTGATCCCATGGCGTACGCTCTCTGgtcgt                                                             <  1:2031250/36‑1 (MQ=255)
                                          cACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCa                                      >  1:4803355/1‑59 (MQ=255)
                                             gAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGAttt                       >  1:2426852/1‑71 (MQ=255)
                                             gAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGAttt                       <  1:4714232/71‑1 (MQ=255)
                                               gCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCg                     <  1:2854667/71‑1 (MQ=255)
                                                cTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGa                                            <  1:1846671/47‑1 (MQ=255)
                                                cTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGa                                            <  1:2412288/47‑1 (MQ=255)
                                                cTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGAATCAGGATCACCAGTGGATGCGTGATTTCgg                    <  1:5682121/71‑1 (MQ=255)
                                                 tGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTg                                                    <  1:2084201/38‑1 (MQ=255)
                                                 tGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTg                                                    <  1:2223350/38‑1 (MQ=255)
                                                 tGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTg                                                    <  1:538502/38‑1 (MQ=255)
                                                 tGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTg                                                    <  1:4889442/38‑1 (MQ=255)
                                                   aTCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATc                                          <  1:5120110/46‑1 (MQ=255)
                                                   aTCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATc                                          <  1:4344398/46‑1 (MQ=255)
                                                   aTCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGa                 <  1:3230051/71‑1 (MQ=255)
                                                    tCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATc                                          <  1:943826/45‑1 (MQ=255)
                                                     cccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAcc                                       >  1:5323161/1‑47 (MQ=255)
                                                     cccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTg                  >  1:5589866/1‑68 (MQ=255)
                                                     cccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGa                 >  1:1361191/1‑69 (MQ=255)
                                                     cccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGa                 >  1:3302829/1‑69 (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)
                                                         tGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGCct           <  1:1639736/71‑1 (MQ=255)
                                                         tGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGCct           <  1:701343/71‑1 (MQ=255)
                                                         tGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGAGGCGTGCTTTTGGTGAAAGCct           <  1:1222393/71‑1 (MQ=255)
                                                           gCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCctgc         <  1:4569211/71‑1 (MQ=255)
                                                           gCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCctgc         <  1:3485840/71‑1 (MQ=255)
                                                           gCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCctgc         <  1:3837109/71‑1 (MQ=255)
                                                            cGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCctgct        >  1:802042/1‑71 (MQ=255)
                                                             gTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCa                                      >  1:1814474/1‑40 (MQ=255)
                                                              tACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                        <  1:5384262/37‑1 (MQ=255)
                                                              tACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                        <  1:424938/37‑1 (MQ=255)
                                                              tACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                        <  1:181024/37‑1 (MQ=255)
                                                              tACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                        <  1:4558929/37‑1 (MQ=255)
                                                                 gCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGc             >  1:1064415/1‑61 (MQ=255)
                                                                 gCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGc             >  1:274199/1‑61 (MQ=255)
                                                                  ctctctGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTa  <  1:2709479/71‑1 (MQ=255)
                                                                    |                                                                    
GAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTA  >  minE/834591‑834727

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