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 608,772 T→C 27.7% A494A (GCA→GCG)  pflB ← pyruvate formate lyase I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE608,7720TC27.7% 263.0 / 120.0 173A494A (GCA→GCG) pflBpyruvate formate lyase I
Reads supporting (aligned to +/- strand):  ref base T (66/59);  new base C (16/32);  total (82/91)
Fisher's exact test for biased strand distribution p-value = 2.70e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

Only 100 of 213 total aligned reads displayed.

CACGGTCGTGCAGCGCCATCAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATGCGCTCCATCACTTCATCATAGTTC  >  minE/608702‑608841
                                                                      |                                                                     
cACGGTCGTGCAGCGCCATCAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTcagt                                                                       >  1:3647712/1‑71 (MQ=255)
 aCGGTCGTGCAGCGCCATCAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTcagtg                                                                      >  1:3543678/1‑71 (MQ=255)
 aCGGTCGTGCAGCGCCATCAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTcagtg                                                                      >  1:2192726/1‑71 (MQ=255)
 aCGGTCGTGCAGCGCCATCAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTcagtg                                                                      >  1:2256811/1‑71 (MQ=255)
 aCGGTCGTGCAGCGCCATCAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTcagtg                                                                      >  1:3045651/1‑71 (MQ=255)
    gttgTGCAGCGCCATCAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTcagtgcag                                                                   <  1:4200103/68‑1 (MQ=255)
    gTCGTGCAGCGCCATCAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTcagtgcag                                                                   >  1:3504231/1‑71 (MQ=255)
    gTCGTGCAGCGCCATCAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTcagtgcag                                                                   >  1:2970207/1‑71 (MQ=255)
     tCGTGCAGCGCCATCAGCGAAGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGAATGATATTcagcgcgct                                                                  <  1:5602762/71‑4 (MQ=255)
     tCGTGCAGCGCCATCAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTcagtgcagt                                                                  >  1:1684569/1‑71 (MQ=255)
     tCGTGCAGCGCCATCAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTcagtgcagt                                                                  <  1:79426/71‑1 (MQ=255)
       gTGCAGCGCCATCAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGa                                                                >  1:1885736/1‑71 (MQ=255)
         gCAGCGCCATCAGCGAAGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGAATGATATTCAGCGCGCTGATg                                                              >  1:5679924/1‑71 (MQ=255)
         gCAGCGCCATCAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATg                                                              >  1:755507/1‑71 (MQ=255)
          cAGCGCCATCAGCGAAGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGAATGATATTCAGCGCGCTGATg                                                              <  1:4888514/70‑1 (MQ=255)
          cAGCGCCATCAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATg                                                              >  1:1228218/1‑70 (MQ=255)
          cAGCGCCATCAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATg                                                              <  1:2351756/70‑1 (MQ=255)
             cgcCATCAGCGAAGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGAATGATATTCAGCGCGCTGATGTACt                                                          <  1:2579433/71‑1 (MQ=255)
             cgcCATCAGCGAAGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGAATGATATTCAGCGCGCTGATGTACt                                                          <  1:1975400/71‑1 (MQ=255)
              gcCATCAGAGAGTCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTg                                                         <  1:3744199/71‑1 (MQ=255)
                cATCAGCGAAGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGAATGATATTCAGCGCGCTGATGTACTgca                                                       <  1:1111821/71‑3 (MQ=255)
                cATCAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTg                                                         >  1:2101143/1‑69 (MQ=255)
                 aTCAGCGAAGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGAATGATATTCAGCGCGCTGATGTACTgcac                                                      <  1:4290162/71‑4 (MQ=255)
                  tCAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTcagtgca                                                                    <  1:5468068/56‑1 (MQ=255)
                   cAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTag                                                    >  1:1534630/1‑71 (MQ=255)
                    agagagGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGtt                                                       >  1:2912605/1‑67 (MQ=255)
                       gagGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTagccag                                                >  1:974728/1‑71 (MQ=255)
                        agGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTcagtg                                                                      <  1:928533/48‑1 (MQ=255)
                        agGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTcagtg                                                                      <  1:2750183/48‑1 (MQ=255)
                                tAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTa                                                     <  1:5263774/57‑1 (MQ=255)
                                  gCTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGa                                                                >  1:4110529/1‑44 (MQ=255)
                                  gCTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTagccagc                                               <  1:824590/61‑1 (MQ=255)
                                  gCTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTagccagc                                               <  1:5332163/61‑1 (MQ=255)
                                  gCTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATg                                      >  1:5101739/1‑70 (MQ=255)
                                  gCTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATg                                      >  1:4338760/1‑70 (MQ=255)
                                  gCTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGa                                     <  1:4621071/71‑1 (MQ=255)
                                   cTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATg                                      >  1:3284711/1‑69 (MQ=255)
                                    tGTACTTGTCGTGCATGTAGTGAATGATATTcagcgc                                                                     >  1:4978199/1‑37 (MQ=25)
                                    tGTACTTGTCGTGCATGTAGTGAATGATATTcagcgc                                                                     >  1:119248/1‑37 (MQ=25)
                                    tGTACTTGTCGTGCATGTAGTGAATGATATTcagcgc                                                                     >  1:3580657/1‑37 (MQ=25)
                                     gTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGt                                                        <  1:988713/49‑1 (MQ=255)
                                      tACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTagc                                                   <  1:565187/53‑1 (MQ=255)
                                      tACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTagc                                                   <  1:1791742/53‑1 (MQ=255)
                                      tACTTGTCGTGCATGTAGTGAATGATATTCAGCGCGCTGATGTACTGCACCGCCAGCCAGTCCATGAAGTg                                 <  1:4662897/71‑1 (MQ=255)
                                       aCTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGa                                >  1:538167/1‑71 (MQ=255)
                                       aCTTGTCGTGCATGTAGTGAATGATATTCAGCGCGCTGATGTACTgca                                                       <  1:912092/48‑3 (MQ=255)
                                        cTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTagc                                                   <  1:4455116/51‑1 (MQ=255)
                                        cTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGAt                               <  1:628207/71‑1 (MQ=255)
                                         ttGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTagcca                                                 <  1:284552/52‑1 (MQ=255)
                                         ttGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTagcca                                                 <  1:3823966/52‑1 (MQ=255)
                                         ttGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATc                              >  1:5420974/1‑71 (MQ=255)
                                         ttGTCGTGCATGTAGTGAATGATATTCAGCGCGCTGATg                                                              <  1:2321909/39‑1 (MQ=16)
                                         ttGTCGTGCATGTAGTGAATGATATTCAGCGCGCTGATg                                                              <  1:2957964/39‑1 (MQ=16)
                                          tGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTagcca                                                 >  1:317845/1‑51 (MQ=255)
                                          tGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGAt                               >  1:417894/1‑69 (MQ=255)
                                          tGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGAt                               >  1:3394917/1‑69 (MQ=255)
                                          tGTCGTGCATGTAGTGGATGATGTTCACTGCAGTGATGTACTGTTTagcca                                                 >  1:395611/1‑51 (MQ=255)
                                           gTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATcc                             <  1:2236535/70‑1 (MQ=255)
                                           gTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCa                            >  1:3310956/1‑71 (MQ=255)
                                           gTCGTGCATGTAGTGAATGATATTCAGCGCGCTGATGTACTGCACCGCCAGCCAGTcc                                         <  1:481885/58‑1 (MQ=255)
                                           gTCGTGCATGTAGTGAATGATATTCAGCGCGCTGATGTACTGCACCGCCAGCCAGTCCATGAAGTGATc                              <  1:2454362/69‑1 (MQ=255)
                                            tCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATc                              <  1:3352880/68‑1 (MQ=255)
                                            tCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCAt                           >  1:4930906/1‑71 (MQ=255)
                                            tCGTGCATGTAGTGAATGATATTCAGCGCGCTGATGTACTGCACCGCCAGCCAGTCCATGAAGTGATcga                            <  1:2636195/70‑3 (MQ=255)
                                             cGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATg                          >  1:5019723/1‑71 (MQ=255)
                                              gTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGt                                                        >  1:2618236/1‑40 (MQ=255)
                                              gTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGt                                                        >  1:3112656/1‑40 (MQ=255)
                                                gCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTagccagcc                                              <  1:1966901/48‑1 (MQ=255)
                                                 cATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATGCGCt                      >  1:5178894/1‑71 (MQ=255)
                                                 cATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATGCGCt                      <  1:3455623/71‑1 (MQ=255)
                                                   tGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATGCGCTc                     >  1:4003165/1‑70 (MQ=255)
                                                     tAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATGCGCTCCa                   <  1:4580983/70‑1 (MQ=255)
                                                     tAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATGCGCTCCAt                  <  1:4527083/71‑1 (MQ=255)
                                                     tAGTGAATGATATTCAGCGCGCTGATGTACTGCACCGCCAGCCAGTCCATGaa                                    >  1:5577554/1‑53 (MQ=12)
                                                     tAGTGAATGATATTCAGCGCGCTGATGTACTGCACCGCCAGCCAGTCCATGAAGTGATc                              <  1:1008395/59‑1 (MQ=255)
                                                     tAGTGAATGATATTCAGCGCGCTGATGTACTGCACCGCCAGCCAGTCCATGAAGTGATc                              <  1:1843464/59‑1 (MQ=255)
                                                       gTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATGCGCTCCATCa                <  1:2696829/71‑1 (MQ=255)
                                                       gTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATGCGCTCCATCa                <  1:3008225/71‑1 (MQ=255)
                                                       gTGAATGATATTCAGCGCGCTGATGTACTGCACCGCCAGCCAGTCCATGAAg                                   <  1:195627/52‑1 (MQ=12)
                                                        tgaatgataTTCAGCGCGCTGATGTACTGCACCGCCAGCCAGTCCATGAAGTGATCGAGGCTGTCCATCAc               <  1:159215/68‑1 (MQ=255)
                                                        tGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGa                                     <  1:879306/49‑1 (MQ=255)
                                                          gatgatGTTCAGTGCAGTGATGTACTGTTTagccag                                                <  1:921637/36‑1 (MQ=255)
                                                          gatgatGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGa                                     >  1:5534629/1‑47 (MQ=255)
                                                          gatgatGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGAt                               >  1:4689700/1‑53 (MQ=255)
                                                          gatgatGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATGCGCTCCATCACt              <  1:2768294/70‑1 (MQ=255)
                                                          aatgataTTCAGCGCGCTGATGTACTGCACCGCCAGCCAGTCCATGAAGTGATCGAGGCTGTCCATCACtt             >  1:1423752/2‑71 (MQ=255)
                                                           atgataTTCAGCGCGCTGATGTACTGCACCGCCAGCCAGTCCATGAAGTGATCGAGGCTGTCCATCACttt            <  1:4779975/71‑2 (MQ=255)
                                                            tgatgTTCAGTGCAGTGATGTACTGTTTACCCAGCCAGTCCATGAAGTGATCCATGCGCTCCATCACTtca           <  1:2401335/71‑1 (MQ=255)
                                                            tgataTTCAGCGCGCTGATGTACTGCACCGCCAGCCAGTCCATGAAGTGATCGAGGCTGTCCATCACtttg           <  1:1182116/71‑3 (MQ=255)
                                                            tgataTTCAGCGCGCTGATGTACTGCACCGCCAGCCAGTCCATGAAGTGATCGAGGCTGTCCATCACtttg           >  1:3939805/1‑69 (MQ=255)
                                                               tgTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATg                                      <  1:5018171/41‑1 (MQ=255)
                                                               tgTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATGCGCTCCATCACTtcatca        <  1:472241/71‑1 (MQ=255)
                                                               tgTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATGCGCTCCATCACTtcatca        <  1:1855108/71‑1 (MQ=255)
                                                                 ttCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATGCGCTCCATCACTtcatca        >  1:5059907/1‑69 (MQ=255)
                                                                  tCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATGCGCTCCATCACTtcat          >  1:1206162/1‑66 (MQ=255)
                                                                  tCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATGCGCTCCATCACTTCATCATAg     >  1:1383646/1‑71 (MQ=255)
                                                                   cagtgcagtgATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATGCGCTCCATCACTTCATCATAg     >  1:528916/1‑70 (MQ=255)
                                                                   cagtgcagtgATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATGCGCTCCATCACTTCATCATAg     >  1:2147734/1‑70 (MQ=255)
                                                                     gtgcagtgATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATGCGCTCCATCACTTCATCATAGTTc  <  1:1142408/71‑1 (MQ=255)
                                                                      tgcagtgATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATcc                             <  1:660559/43‑1 (MQ=255)
                                                                      |                                                                     
CACGGTCGTGCAGCGCCATCAGAGAGGCTTCGTAGCTGTACTTGTCGTGCATGTAGTGGATGATGTTCAGTGCAGTGATGTACTGTTTAGCCAGCCAGTCCATGAAGTGATCCATGCGCTCCATCACTTCATCATAGTTC  >  minE/608702‑608841

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