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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,478,336 T→C 31.5% F103F (TTT→TTC)  pstB → phosphate transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,478,3360TC31.5% 97.1 / 59.0 114F103F (TTT→TTC) pstBphosphate transporter subunit
Reads supporting (aligned to +/- strand):  ref base T (30/48);  new base C (21/15);  total (51/63)
Fisher's exact test for biased strand distribution p-value = 6.77e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 119 total aligned reads displayed.

AACTCTCAGGATATCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGAAGCTCTCCCGTGCCGACA  >  minE/2478271‑2478403
                                                                 |                                                                   
aaCTCTCAGGATATCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCg                                                                  >  1:3297931/1‑69 (MQ=255)
aaCTCTCAGGATATCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCg                                                                  >  1:291837/1‑69 (MQ=255)
aaCTCTCAGGATATCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCg                                                                  >  1:3138597/1‑69 (MQ=255)
aaCTCTCAGGATATCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCg                                                                  >  1:500033/1‑69 (MQ=255)
       aGGATATCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCa                                                           >  1:1075137/1‑69 (MQ=255)
         gATATCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCa                                                           <  1:1911965/67‑1 (MQ=255)
         gATATCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCa                                                           <  1:3354550/67‑1 (MQ=255)
         gATATCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATc                                                         <  1:2794215/69‑1 (MQ=255)
          atatCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCa                                                           <  1:410131/66‑1 (MQ=255)
          atatCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATc                                                         <  1:2380047/68‑1 (MQ=255)
           tatCGCACTGCTTCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTcc                                                            <  1:2701860/64‑1 (MQ=255)
             tCGCACTTCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACg                                                     <  1:1435715/69‑1 (MQ=255)
             tCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATCTAc                                                      >  1:2158630/1‑68 (MQ=255)
             tCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATCTAc                                                      >  1:3287682/1‑68 (MQ=255)
             tCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATCTAc                                                      >  1:2514945/1‑68 (MQ=255)
             tCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACg                                                     <  1:112344/69‑1 (MQ=255)
             tCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACg                                                     <  1:321303/69‑1 (MQ=255)
             tCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACg                                                     <  1:1538540/69‑1 (MQ=255)
             tCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACg                                                     <  1:1607191/69‑1 (MQ=255)
             tCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACg                                                     <  1:243806/69‑1 (MQ=255)
             tCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACg                                                     <  1:247182/69‑1 (MQ=255)
              cGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACg                                                     <  1:2799638/68‑1 (MQ=255)
              cGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACg                                                     <  1:325345/68‑1 (MQ=255)
                    gctgcGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGacaaca                                               >  1:484944/1‑68 (MQ=255)
                    gctgcGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACAt                                              >  1:495060/1‑69 (MQ=255)
                    gctgcGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACAt                                              >  1:1251749/1‑69 (MQ=255)
                    gctgcGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACAt                                              >  1:3242595/1‑69 (MQ=255)
                       gcgtgcgAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTCCCAATGTCCATCTACGACAACATCGc                                           >  1:2557797/1‑69 (MQ=255)
                       gcgtgcgAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTCCCAATGTCCATCTACGACAACATCGc                                           >  1:2601063/1‑69 (MQ=255)
                       gcgtgcgAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTCCCAATGTCCATCTACGACAACATCGc                                           >  1:2740156/1‑69 (MQ=255)
                       gcgtgcgAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTCCCAATGTCCATCTACGACAACATCGc                                           >  1:2431244/1‑69 (MQ=255)
                       gcgtgcgAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTCCCAATGTCCATCTACGACAACATCGc                                           >  1:2778535/1‑69 (MQ=255)
                       gcgtgcgAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTCCCAATGTCCATCTACGACAACATCGc                                           >  1:3041541/1‑69 (MQ=255)
                       gcgtgcgAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTCCCAATGTCCATCTACGACAACATCGc                                           >  1:2260807/1‑69 (MQ=255)
                       gcgtgcgAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTCCCAATGTCCATCTACGACAACATCGc                                           >  1:733348/1‑69 (MQ=255)
                       gcgtgcgAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTCCCAATGTCCATCTACGACAACATCGc                                           >  1:937963/1‑69 (MQ=255)
                       gcgtgcgAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTCCCAATGTCCATCTACGACAACATCGc                                           >  1:1050666/1‑69 (MQ=255)
                       gcgtgcgAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTCCCAATGTCCATCTACGACAACATCGc                                           >  1:1067568/1‑69 (MQ=255)
                       gcgtgcgAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTCCCAATGTCCATCTACGACAACATCGc                                           >  1:876702/1‑69 (MQ=255)
                       gcgtgcgAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTCCCAATGTCCATCTACGACAACATCGc                                           >  1:114828/1‑69 (MQ=255)
                       gcgtgcgAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTCCCAATGTCCATCTACGACAACATCGc                                           >  1:1472447/1‑69 (MQ=255)
                       gcgtgcgAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTCCCAATGTCCATCTACGACAACATCGc                                           >  1:2234075/1‑69 (MQ=255)
                       gcgtgcgAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTCCCAATGTCCATCTACGACAACATCGc                                           >  1:1856444/1‑69 (MQ=255)
                       gcgtgcgAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTCCCAATGTCCATCTACGACAACATCGc                                           >  1:2019908/1‑69 (MQ=255)
                                          gtgtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACATCATCGCTTTTGGCGTTCGTCTGt                          >  1:1229997/1‑67 (MQ=255)
                                          gtgtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTg                           >  1:1419036/1‑66 (MQ=255)
                                          gtgtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGttt                        <  1:2474945/69‑1 (MQ=255)
                                          gtgtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGttt                        <  1:897785/69‑1 (MQ=255)
                                          gtgtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGttt                        <  1:735968/69‑1 (MQ=255)
                                          gtgtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGttt                        <  1:581909/69‑1 (MQ=255)
                                          gtgtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGttt                        <  1:3396828/69‑1 (MQ=255)
                                          gtgtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGttt                        <  1:2524008/69‑1 (MQ=255)
                                          gtgtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGt                          >  1:2626364/1‑67 (MQ=255)
                                          gtgtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGt                          >  1:3246601/1‑67 (MQ=255)
                                          gtgtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGt                          >  1:2402123/1‑67 (MQ=255)
                                            gtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCt                            <  1:3036037/63‑1 (MQ=255)
                                            gtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCt                            <  1:2028598/63‑1 (MQ=255)
                                            gtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCt                            <  1:602491/63‑1 (MQ=255)
                                            gtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCt                            <  1:3163640/63‑1 (MQ=255)
                                            gtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCt                            <  1:1743669/63‑1 (MQ=255)
                                            gtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCt                            <  1:1392292/63‑1 (MQ=255)
                                            gtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCt                            <  1:1834296/63‑1 (MQ=255)
                                            gtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCt                            <  1:2010175/63‑1 (MQ=255)
                                            gtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCt                            <  1:1989070/63‑1 (MQ=255)
                                            gtTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCt                            <  1:1649314/63‑1 (MQ=255)
                                               ccAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGaa                   >  1:3014335/1‑69 (MQ=255)
                                               ccAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGaa                   >  1:3312004/1‑69 (MQ=255)
                                               ccAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGaa                   >  1:745476/1‑69 (MQ=255)
                                               ccAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGaa                   >  1:2719627/1‑69 (MQ=255)
                                               ccAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGaa                   >  1:3297080/1‑69 (MQ=255)
                                               ccAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGaa                   >  1:2258316/1‑69 (MQ=255)
                                                     aCCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGAAGCtctc             >  1:1018911/1‑69 (MQ=255)
                                                     aCCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGAAGCtctc             >  1:108628/1‑69 (MQ=255)
                                                        gACGCCGTTCCCAATGTCCATCTACGACAACATCGCTTTTGGCGTGCGTCTGTTTGAGAAGCTCTCCCg          <  1:966883/69‑1 (MQ=255)
                                                        gACGCCGTTCCCAATGTCCATCTACGACAACATCGCTTTTGGCGTGCGTCTGTTTGAGAAGCTCTCCCg          <  1:759340/69‑1 (MQ=255)
                                                        gACGCCGTTCCCAATGTCCATCTACGACAACATCGCTTTTGGCGTGCGTCTGTTTGAGAAGCTCTCCCg          <  1:1128131/69‑1 (MQ=255)
                                                        gACGCCGTTCCCAATGTCCATCTACGACAACATCGCTTTTGGCGTGCGTCTGTTTGAGAAGCTCTCCCg          <  1:1519146/69‑1 (MQ=255)
                                                        gACGCCGTTCCCAATGTCCATCTACGACAACATCGCTTTTGGCGTGCGTCTGTTTGAGAAGCTCTCCCg          <  1:1018086/69‑1 (MQ=255)
                                                        gACGCCGTTCCCAATGTCCATCTACGACAACATCGCTTTTGGCGTGCGTCTGTTTGAGAAGCTCTCCCg          <  1:646796/69‑1 (MQ=255)
                                                        gACGCCGTTCCCAATGTCCATCTACGACAACATCGCTTTTGGCGTGCGTCTGTTTGAGAAGCTCTCCCg          <  1:1853013/69‑1 (MQ=255)
                                                        gACGCCGTTCCCAATGTCCATCTACGACAACATCGCTTTTGGCGTGCGTCTGTTTGAGAAGCTCTCCCg          <  1:2061314/69‑1 (MQ=255)
                                                        gACGCCGTTCCCAATGTCCATCTACGACAACATCGCTTTTGGCGTGCGTCTGTTTGAGAAGCTCTCCCg          <  1:959539/69‑1 (MQ=255)
                                                        gACGCCGTTCCCAATGTCCATCTACGACAACATCGCTTTTGGCGTGCGTCTGTTTGAGAAGCTCTCCCg          <  1:443801/69‑1 (MQ=255)
                                                        gACGCCGTTCCCAATGTCCATCTACGACAACATCGCTTTTGGCGTGCGTCTGTTTGAGAAGCTCTCCCg          <  1:2435200/69‑1 (MQ=255)
                                                        gACGCCGTTCCCAATGTCCATCTACGACAACATCGCTTTTGGCGTGCGTCTGTTTGAGAAGCTCTCCCg          <  1:2542581/69‑1 (MQ=255)
                                                        gACGCCGTTCCCAATGTCCATCTACGACAACATCGCTTTTGGCGTGCGTCTGTTTGAGAAGCTCTCCCg          <  1:2766118/69‑1 (MQ=255)
                                                        gACGCCGTTCCCAATGTCCATCTACGACAACATCGCTTTTGGCGTGCGTCGGTTTGAGAAGCTCTCCCg          <  1:2393645/69‑1 (MQ=255)
                                                              gTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGAAGCTCTCCCGTGCCGa    <  1:495040/69‑1 (MQ=255)
                                                              gTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGAAGCTCTCCCGTGCCGa    <  1:2233484/69‑1 (MQ=255)
                                                              gTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGAAGCTCTCCCGTGCCGa    <  1:580950/69‑1 (MQ=255)
                                                              gTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGAAGCTCTCCCGTGCCGa    <  1:3077737/69‑1 (MQ=255)
                                                              gTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGAAGCTCTCCCGTGCCGa    <  1:3387857/69‑1 (MQ=255)
                                                              gTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGAAGCTCTCCCGTGCCGa    <  1:1164703/69‑1 (MQ=255)
                                                              gTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGAAGCTCTCCCGTGCCGa    <  1:3361053/69‑1 (MQ=255)
                                                              gTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGAAGCTCTCCCGTGCCGa    <  1:835929/69‑1 (MQ=255)
                                                               tttCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGAAGCTCTCCCGTGCCGa    <  1:1076722/68‑1 (MQ=255)
                                                                 tCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGAAGCTCTCCCGTGCCGACa  >  1:191237/1‑68 (MQ=255)
                                                                 tCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGAAGCTCTCCCGTGCCGACa  >  1:64761/1‑68 (MQ=255)
                                                                 tCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGAAGCTCTCCCGTGCCGACa  >  1:445817/1‑68 (MQ=255)
                                                                 tCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGAAGCTCTCCCGTGCCGACa  >  1:3338946/1‑68 (MQ=255)
                                                                 |                                                                   
AACTCTCAGGATATCGCACTGCTGCGTGCGAAAGTGGGCATGGTGTTCCAGAAACCGACGCCGTTTCCGATGTCCATCTACGACAACATCGCTTTTGGCGTTCGTCTGTTTGAGAAGCTCTCCCGTGCCGACA  >  minE/2478271‑2478403

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