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 835,233 A→G 22.6% I1231V (ATT→GTT)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,2330AG22.6% 247.5 / 72.6 137I1231V (ATT→GTT) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base A (52/54);  new base G (14/17);  total (66/71)
Fisher's exact test for biased strand distribution p-value = 8.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

Only 100 of 142 total aligned reads displayed.

CGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGT  >  minE/835163‑835302
                                                                      |                                                                      
cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                                                                        >  1:5614683/1‑71 (MQ=255)
cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                                                                        <  1:5282743/71‑1 (MQ=255)
   cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                                                                      >  1:3862488/1‑70 (MQ=255)
    tttAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGtt                                                                      <  1:2956660/69‑1 (MQ=255)
       aaCTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACt                                                                  <  1:3100500/70‑1 (MQ=255)
        actactATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAt                                                                       >  1:3442705/1‑64 (MQ=255)
        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                                                               >  1:4961987/1‑68 (MQ=255)
            ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                                               >  1:5368718/1‑68 (MQ=255)
              acggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                                                          >  1:256060/3‑71 (MQ=255)
              acggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAACAACGTTAACTGGCTGGAt                                                          >  1:359637/3‑71 (MQ=255)
               tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                                                                        <  1:5095584/56‑1 (MQ=255)
               tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                                           <  1:1103606/69‑1 (MQ=255)
               tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                                                         >  1:5242741/1‑71 (MQ=255)
               tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                                                         >  1:1580240/1‑71 (MQ=255)
               tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                                                         >  1:1344664/1‑71 (MQ=255)
               cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGttaa                                                                    >  1:5650863/2‑58 (MQ=255)
               cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGttaa                                                                    >  1:2452135/2‑58 (MQ=255)
               cggCACCGTCGGATCGAACCGCGATGAGCTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                                                          >  1:283218/2‑70 (MQ=255)
                ggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATga                                                        <  1:5684417/71‑2 (MQ=255)
                 gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat                                                       >  1:227615/1‑69 (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)
                  cACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat                                                       >  1:3810990/1‑68 (MQ=255)
                  cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAg                                                            >  1:1898385/1‑65 (MQ=255)
                  cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAg                                                            >  1:5296291/1‑65 (MQ=255)
                  cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCg                                                      <  1:2292372/71‑1 (MQ=255)
                  cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCg                                                      <  1:2319062/71‑1 (MQ=255)
                   aCCGTAGGTTGTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCg                                                      <  1:4327716/70‑1 (MQ=255)
                    ccGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCg                                                      >  1:2935844/1‑69 (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)
                       tAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                                                                        >  1:3197425/1‑48 (MQ=255)
                          gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                                                                      <  1:30916/47‑1 (MQ=255)
                          gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                                              <  1:959522/71‑1 (MQ=255)
                          gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                                              <  1:4239680/71‑1 (MQ=255)
                           ttCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa                                                     <  1:3286952/63‑1 (MQ=255)
                           ttCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa                                                     <  1:1123275/63‑1 (MQ=255)
                            tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                                           >  1:4934101/1‑56 (MQ=255)
                            tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                                           >  1:4039788/1‑56 (MQ=255)
                            tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGc                                                       <  1:4522556/60‑1 (MQ=255)
                            tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGc                                                       <  1:1346366/60‑1 (MQ=255)
                             cTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                                           >  1:2503013/1‑71 (MQ=255)
                             cTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                                           >  1:340032/1‑71 (MQ=255)
                              tAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                                             <  1:628252/52‑1 (MQ=255)
                              tAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                                           >  1:4231039/1‑70 (MQ=255)
                               aaCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                                           >  1:5509325/1‑69 (MQ=255)
                                aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGa                                            <  1:2149009/67‑1 (MQ=255)
                                aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                                           <  1:1694742/68‑1 (MQ=255)
                                aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                                           <  1:1877255/68‑1 (MQ=255)
                                aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                                           <  1:4592101/68‑1 (MQ=255)
                                aCCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc                                                                   >  1:3547809/1‑44 (MQ=255)
                                 ccGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATg                                                         <  1:2007834/53‑1 (MQ=255)
                                   gcgATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTa                                     <  1:3591986/71‑1 (MQ=255)
                                    cgATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTa                                     >  1:3728797/1‑70 (MQ=255)
                                           tttGTTGTAGTGCGTAAGATGAAGAACATTGACTg                                                                 <  1:4366415/35‑1 (MQ=255)
                                            ttgttgTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                                           <  1:1614334/40‑1 (MQ=255)
                                             tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAg                                                            >  1:5434985/1‑38 (MQ=255)
                                             tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAg                                                            >  1:786608/1‑38 (MQ=255)
                                             tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt                                                          >  1:4855383/1‑40 (MQ=255)
                                             tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCaa                                               >  1:4375949/1‑51 (MQ=255)
                                             tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCg                           >  1:3439300/1‑71 (MQ=255)
                                                 gtAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt                                                          >  1:3267547/1‑36 (MQ=255)
                                                 gtAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt                                                          >  1:4466483/1‑36 (MQ=255)
                                                    gTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGaa                                                    >  1:4810196/1‑39 (MQ=255)
                                                     tGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAcc                                          <  1:795173/48‑1 (MQ=255)
                                                     tGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATg                   >  1:4763152/1‑70 (MQ=255)
                                                     tGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGa                  <  1:2664627/71‑1 (MQ=255)
                                                       cGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGaa                 >  1:3055297/1‑70 (MQ=255)
                                                       cGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGaa                 <  1:5539812/70‑1 (MQ=255)
                                                         tAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCa                                         >  1:1141528/1‑45 (MQ=255)
                                                         tAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAg                                        >  1:4921519/1‑46 (MQ=255)
                                                         caaGATGAAGAACGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCGAAAAAATGaaa                <  1:2403104/68‑1 (MQ=255)
                                                          aaGATGAAGAACGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCGAAAAAATGAAAAt              <  1:1966250/70‑1 (MQ=255)
                                                             aTGAAGAACATTGACTGGTTAGATGGCGAAGGCaa                                               >  1:2097997/1‑35 (MQ=255)
                                                             aTGAAGAACATTGACTGGTTAGATGGCGAAGGCaa                                               >  1:764503/1‑35 (MQ=255)
                                                              tGAAGAACGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCG‑Aaaaaa                    <  1:5013240/59‑2 (MQ=255)
                                                              tGAAGAACGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCG‑Aaaaaa                    <  1:2527413/59‑2 (MQ=255)
                                                              tGAAGAACGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCG‑Aaaaaa                    <  1:3227338/59‑2 (MQ=255)
                                                              tGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGtt         <  1:5153314/71‑1 (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)
                                                                 agaaCGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTca       >  1:782842/1‑70 (MQ=255)
                                                                 agaaCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTcac      <  1:3717937/71‑1 (MQ=255)
                                                                 agaaCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTcac      <  1:4669113/71‑1 (MQ=255)
                                                                  gaaCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAg                                  <  1:3545794/43‑1 (MQ=255)
                                                                  gaaCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTcaca     <  1:1974923/71‑1 (MQ=255)
                                                                    aCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGaaaa               >  1:338585/1‑59 (MQ=255)
                                                                    aCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGaaaa               >  1:3805091/1‑59 (MQ=255)
                                                                    aCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGaaaa               >  1:3944474/1‑59 (MQ=255)
                                                                      |                                                                      
CGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGT  >  minE/835163‑835302

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