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 835,236 G→A 20.3% D1232N (GAC→AAC)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,2360GA20.3% 273.1 / 58.9 133D1232N (GAC→AAC) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base G (50/56);  new base A (12/15);  total (62/71)
Fisher's exact test for biased strand distribution p-value = 8.32e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01

Only 100 of 134 total aligned reads displayed.

AACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGG  >  minE/835170‑835305
                                                                  |                                                                      
 actactATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACt                                                                     <  1:5176581/69‑1 (MQ=255)
 actactATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTgg                                                                   <  1:4961804/71‑1 (MQ=255)
  ctactaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTgg                                                                   <  1:4001945/70‑1 (MQ=255)
  ctactaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                                                  <  1:2812972/71‑1 (MQ=255)
  ctactaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                                                  <  1:105446/71‑1 (MQ=255)
  ctactaCGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTggc                                                                  <  1:3275169/71‑2 (MQ=255)
     ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                                                  >  1:5368718/1‑68 (MQ=255)
       acggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                                                             >  1:256060/3‑71 (MQ=255)
       acggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAACAACGTTAACTGGCTGGAt                                                             >  1:359637/3‑71 (MQ=255)
        tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                                              <  1:1782557/69‑1 (MQ=255)
        tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                                              <  1:1230388/69‑1 (MQ=255)
        tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                                              <  1:1103606/69‑1 (MQ=255)
        tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                                                            >  1:1580240/1‑71 (MQ=255)
        tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                                                            >  1:1344664/1‑71 (MQ=255)
        cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                                                             <  1:4956914/69‑1 (MQ=255)
        cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                                                             <  1:3390824/69‑1 (MQ=255)
        cggCACCGTCGGATCGAACCGCGATGAGCTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                                                             >  1:283218/2‑70 (MQ=255)
         ggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATga                                                           <  1:5684417/71‑2 (MQ=255)
          gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat                                                          >  1:227615/1‑69 (MQ=255)
          gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat                                                          >  1:2619988/1‑69 (MQ=255)
          gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATga                                                           >  1:5190126/1‑69 (MQ=255)
          gCACCGTCGGATCGAACCGCGATGACTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat                                                          <  1:733046/71‑3 (MQ=255)
          gCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGAc                                                                      >  1:3683516/1‑59 (MQ=255)
          gCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATgg                                                           <  1:5495953/70‑1 (MQ=255)
          gCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATgg                                                           <  1:5209487/70‑1 (MQ=255)
           cACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat                                                          >  1:3810990/1‑68 (MQ=255)
           cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGTAGAACATTGACTGGTTAGATGGCg                                                         <  1:2297451/71‑1 (MQ=255)
           cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAg                                                               >  1:5296291/1‑65 (MQ=255)
           cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAg                                                               >  1:1898385/1‑65 (MQ=255)
           cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCg                                                         <  1:2319062/71‑1 (MQ=255)
            aCCGTAGGTTGTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCg                                                         <  1:4327716/70‑1 (MQ=255)
              cGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTgg                                                                   <  1:3136321/58‑1 (MQ=255)
               gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGGAGAACATTGACTGGTTa                                                                >  1:2039359/1‑60 (MQ=255)
               gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                                                >  1:1116169/1‑60 (MQ=255)
               gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAgg                                                     >  1:932341/1‑71 (MQ=255)
                   gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                                                <  1:1946457/56‑1 (MQ=255)
                   gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                                                <  1:5485123/56‑1 (MQ=255)
                   gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                                                 <  1:959522/71‑1 (MQ=255)
                    ttCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa                                                        <  1:1123275/63‑1 (MQ=255)
                    ttCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa                                                        <  1:3286952/63‑1 (MQ=255)
                     tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                                              >  1:4934101/1‑56 (MQ=255)
                     tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                                              >  1:4039788/1‑56 (MQ=255)
                     tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGc                                                          <  1:1346366/60‑1 (MQ=255)
                     tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGc                                                          <  1:4522556/60‑1 (MQ=255)
                     tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGa                                               >  1:785147/1‑71 (MQ=255)
                      cTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                                              >  1:340032/1‑71 (MQ=255)
                      cTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                                              >  1:2503013/1‑71 (MQ=255)
                       tAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                                                <  1:4870463/52‑1 (MQ=255)
                       tAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                                              >  1:4231039/1‑70 (MQ=255)
                        aaCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                                              >  1:5509325/1‑69 (MQ=255)
                         aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                                              <  1:4227824/52‑1 (MQ=255)
                         aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGa                                               <  1:2149009/67‑1 (MQ=255)
                         aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAcc                                             <  1:5054707/69‑1 (MQ=255)
                         aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                                              <  1:1694742/68‑1 (MQ=255)
                         aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                                              <  1:4592101/68‑1 (MQ=255)
                         aCCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc                                                                      >  1:3547809/1‑44 (MQ=255)
                         aCCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc                                                                      >  1:657043/1‑44 (MQ=255)
                          ccGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATg                                                            <  1:2007834/53‑1 (MQ=255)
                            gcgATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTa                                        <  1:3591986/71‑1 (MQ=255)
                            gcgATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTa                                        >  1:2143009/1‑71 (MQ=255)
                             cgATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTa                                        >  1:3728797/1‑70 (MQ=255)
                             cgATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTAc                                       <  1:2486915/71‑1 (MQ=255)
                              gATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTa                                        >  1:5679238/1‑69 (MQ=255)
                                    tttGTTGTAGTGCGTAAGATGAAGAACATTGACTg                                                                    <  1:3443788/35‑1 (MQ=255)
                                    tttGTTGTAGTGCGTAAGATGAAGAACATTGACTg                                                                    <  1:4366415/35‑1 (MQ=255)
                                     ttgttgTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                                              <  1:1614334/40‑1 (MQ=255)
                                      tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAg                                                               >  1:786608/1‑38 (MQ=255)
                                      tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt                                                             >  1:4855383/1‑40 (MQ=255)
                                          gtAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt                                                             >  1:4466483/1‑36 (MQ=255)
                                          gtAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt                                                             >  1:3267547/1‑36 (MQ=255)
                                             gTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGaa                                                       >  1:4810196/1‑39 (MQ=255)
                                              tGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAcc                                             <  1:795173/48‑1 (MQ=255)
                                              tGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATg                      >  1:4763152/1‑70 (MQ=255)
                                                cGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGaa                    >  1:3055297/1‑70 (MQ=255)
                                                cGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGaa                    <  1:2785236/70‑1 (MQ=255)
                                                  tAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCa                                            >  1:1141528/1‑45 (MQ=255)
                                                  tAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAgg                                    >  1:2007955/1‑53 (MQ=255)
                                                  tAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAgg                                    >  1:3121267/1‑53 (MQ=255)
                                                  caaGATGAAGAACGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCGAAAAAATGaaa                   <  1:2403104/68‑1 (MQ=255)
                                                   aaGATGAAGAACGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCGAAAAAATGAAAAt                 <  1:1966250/70‑1 (MQ=255)
                                                      aTGAAGAACATTGACTGGTTAGATGGCGAAGGCaa                                                  >  1:764503/1‑35 (MQ=255)
                                                      aTGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGt             >  1:3081228/1‑71 (MQ=255)
                                                       tGAAGAACGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCG‑Aaaaaa                       <  1:5013240/59‑2 (MQ=255)
                                                       tGAAGAACGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCG‑Aaaaaa                       <  1:3227338/59‑2 (MQ=255)
                                                       tGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGtt            <  1:5153314/71‑1 (MQ=255)
                                                       tGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGtt            <  1:4242196/71‑1 (MQ=255)
                                                       tGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGt             >  1:5310696/1‑70 (MQ=255)
                                                        gaagaaCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGtt            >  1:2637404/1‑70 (MQ=255)
                                                         aagaaCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTc           <  1:4134869/70‑1 (MQ=255)
                                                          agaaCGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTcac         <  1:2320362/71‑1 (MQ=255)
                                                          agaaCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTcac         <  1:4669113/71‑1 (MQ=255)
                                                          agaaCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTcac         <  1:3717937/71‑1 (MQ=255)
                                                           gaaCGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTcaca        <  1:3837257/71‑1 (MQ=255)
                                                           gaaCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAg                                     <  1:3545794/43‑1 (MQ=255)
                                                           gaaCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTcaca        <  1:5561609/71‑1 (MQ=255)
                                                             aCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGaaaa                  >  1:3805091/1‑59 (MQ=255)
                                                             aCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGaaaa                  >  1:338585/1‑59 (MQ=255)
                                                              cATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGt     >  1:4031414/1‑71 (MQ=255)
                                                                ttGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATg                      <  1:4468078/52‑1 (MQ=255)
                                                                ttGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATg                      <  1:3000606/52‑1 (MQ=255)
                                                                  |                                                                      
AACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGG  >  minE/835170‑835305

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