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 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,571,178 G→C 18.1% R361R (CGG→CGC)  yibH → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,571,1780GC18.1% 268.9 / 48.2 121R361R (CGG→CGC) yibHhypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (52/47);  new base C (14/8);  total (66/55)
Fisher's exact test for biased strand distribution p-value = 4.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

Only 100 of 126 total aligned reads displayed.

CTTACCCGACGGCATCTACGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGATCATTGAGGGGGAGGGGGGAGAT  >  minE/2571109‑2571248
                                                                     |                                                                      
cTTACCCGACGGCATCTACGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGa                                                                       <  1:707775/71‑1 (MQ=255)
  tACCCGACGGCATCTACGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGa                                                                       >  1:3348979/1‑69 (MQ=255)
   aCCCGACGGCATCTACGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGaa                                                                      <  1:2904217/69‑1 (MQ=255)
    cccGACGGCATCTACGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGTTGAAAg                                                                    <  1:508836/70‑1 (MQ=255)
    cccGACGGCATCTACGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAg                                                                    <  1:3333110/70‑1 (MQ=255)
      cGACGGCATCTACGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGtgc                                                                 >  1:2823678/1‑71 (MQ=255)
      agACGGTATTTACGCCCAGGTGGCGGTTTACTCTGATCATTTCAGCCATGTCTCGGTGATGCGCAAAGtgc                                                                 >  1:3886495/2‑71 (MQ=255)
       gACGGTATTTACGCCCAGGTGGCGGTTTACTCTGATCATTTCAGCCATGTCTCGGTGATGCGCAAAGtgc                                                                 >  1:1792418/1‑70 (MQ=255)
       gACGGCATCTACGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGtgct                                                                >  1:1197432/1‑71 (MQ=255)
       gACGGCATCTACGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGtgct                                                                >  1:3001520/1‑71 (MQ=255)
         cGGTATTTACGCCCAGGTGGCGGTTTACTCTGATCATTTCAGCCATGTCTCGGTGATGCGCAAAGtgctat                                                              <  1:632030/71‑3 (MQ=255)
         cGGCATCTACGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGa                                                                       <  1:980118/62‑1 (MQ=255)
           gCATCTACGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGCtctgct                                                             <  1:30981/70‑1 (MQ=255)
            cATCTACGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTgctgct                                                             >  1:2786236/1‑69 (MQ=255)
            cATCTACGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTaa                                                           <  1:1314144/71‑1 (MQ=255)
             aTCTACGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGa                                                                       <  1:2312843/58‑1 (MQ=255)
             aTCTACGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGa                                                                       <  1:3723872/58‑1 (MQ=255)
              tttACGCCCAGGTGGCGGTTTACTCTGATCATTTCAGCCATGTCTCGGTGATGCGCAAAGt                                                                   >  1:1605840/3‑61 (MQ=255)
              tttACGCCCAGGTGGCGGTTTACTCTGATCATTTCAGCCATGTCTCGGTGATGCGCAAAGt                                                                   >  1:384371/3‑61 (MQ=255)
                tACGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGtgctg                                                               >  1:1551595/1‑63 (MQ=255)
                tACGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTa                                                            <  1:1914890/66‑1 (MQ=255)
                  cGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATg                                                      <  1:453814/70‑1 (MQ=255)
                  cGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGa                                                     >  1:1161956/1‑71 (MQ=255)
                   gCCCAGGTGGCGGTTTACTCTGATCATTTCAGCCATGTCTCGGTGATGCGCAAAGTGCTATTACGCATGAc                                                    >  1:3320366/1‑71 (MQ=255)
                     ccAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGAc                                                    >  1:1196244/1‑69 (MQ=255)
                     ccAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGAc                                                    >  1:3008480/1‑69 (MQ=255)
                      cAGGTGGCGGTTTACTCTGATCATTTCAGCCATGTCTCGGTGATGCGCaa                                                                      <  1:1407586/50‑1 (MQ=255)
                      cAGGTGGCGGTTTACTCTGATCATTTCAGCCATGTCTCGGTGATGCGCAAAGTGCTATTACGCATGACCAg                                                 >  1:2751226/1‑71 (MQ=255)
                      cAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAg                                                          <  1:2138075/62‑1 (MQ=255)
                      cAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAg                                                          <  1:2218805/62‑1 (MQ=255)
                        ggTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCt                                               <  1:3030388/71‑1 (MQ=255)
                        ggTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCt                                               >  1:1054204/1‑71 (MQ=255)
                        ggTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCCGTGATGCgg                                                                        >  1:277263/1‑46 (MQ=255)
                               gTTTACTCTGATCATTTCAGCCATGTCTCGGTGATGCGCAAAGTGCTATTACGCATGACCAGCt                                               <  1:2082187/64‑1 (MQ=255)
                               gTTTACTCTGATCATTTCAGCCATGTCTCGGTGATGCGCAAAGTGCTATTACGCATGACCAGCTGGGTGc                                         <  1:1996898/70‑1 (MQ=255)
                               gTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGaaa                                                                     <  1:247820/42‑1 (MQ=255)
                               gTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGaaa                                                                     <  1:2786197/42‑1 (MQ=255)
                                tttACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGaaa                                                                     <  1:3604861/41‑1 (MQ=255)
                                 ttACTCCGACCATTTCAGCGATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCAt                                       >  1:1965689/1‑70 (MQ=255)
                                 ttACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGaa                                                                      >  1:579764/1‑39 (MQ=255)
                                 ttACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCAt                                       >  1:1093774/1‑70 (MQ=255)
                                 ttACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCAt                                       >  1:917966/1‑70 (MQ=255)
                                  tACTCTGATCATTTCAGCCATGTCTCGGTGATGCGCAAAGTGCTATTACGCATGACCAg                                                 <  1:1790166/59‑1 (MQ=255)
                                  tACTCTGATCATTTCAGCCATGTCTCGGTGATGCGCAAAGTGCTATTACGCATGACCAGCTGGGTGCATTa                                     >  1:1522456/1‑71 (MQ=255)
                                   aCTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTAt                                    >  1:1135165/1‑71 (MQ=255)
                                   aCTCCGAACATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATg                                          >  1:1763574/1‑65 (MQ=255)
                                    cTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGAc                                                    >  1:397751/1‑54 (MQ=255)
                                    cTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCac                                                 <  1:1950544/57‑2 (MQ=255)
                                    cTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGa                                            >  1:216338/1‑62 (MQ=255)
                                    cTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTAt                                    <  1:3107350/70‑1 (MQ=255)
                                    cTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATc                                   <  1:2534019/71‑1 (MQ=255)
                                     tCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGaa                                                        >  1:3063680/1‑49 (MQ=255)
                                     tCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGaa                                                        >  1:2466234/1‑49 (MQ=255)
                                     tCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGa                                                         <  1:3054275/48‑1 (MQ=255)
                                     tCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGa                                                         <  1:3938729/48‑1 (MQ=255)
                                      ccGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCtt                                 >  1:3791928/1‑71 (MQ=255)
                                        gACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTa                               <  1:3872986/71‑1 (MQ=255)
                                         aCCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGAc                                                    >  1:3422157/1‑49 (MQ=255)
                                         aCCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGAc                                                    >  1:1563447/1‑49 (MQ=255)
                                           cATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTAttt                            <  1:3483817/71‑1 (MQ=255)
                                            aTTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTg                           <  1:653346/71‑1 (MQ=255)
                                            aTTTCAGCCATGTCTCGGTGATGCGCAAAGTGCTATTACGCATGACAAGCTg                                              >  1:1587590/1‑52 (MQ=255)
                                              ttCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGa                         >  1:2111540/1‑71 (MQ=255)
                                              ttCAGCCATGTCTCGGTGATGCGCAAAGTGCTATTACGCATGAc                                                    >  1:64608/1‑44 (MQ=255)
                                              ttCAGCCATGTCTCGGTGATGCGCAAAGTGCTATTACGCATGAc                                                    >  1:2485515/1‑44 (MQ=255)
                                               tCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGAc                                                    >  1:2358875/1‑43 (MQ=255)
                                               tCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAg                                                 <  1:3544517/46‑1 (MQ=255)
                                               tCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGAt                        >  1:2770059/1‑71 (MQ=255)
                                                cAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTAt                                    >  1:894796/1‑58 (MQ=255)
                                                 aGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCt                                               >  1:1398188/1‑46 (MQ=255)
                                                 aGCCATGTTT‑GGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGATCAt                     <  1:326249/71‑1 (MQ=255)
                                                   ccATGTCTCGGTGATGCGCAAAGTGCTATTACGCATGACCAGCTGGGTGCATTACCTTTATCTCGATCa                      <  1:1846212/69‑1 (MQ=255)
                                                    cATGTCTCGGTGATGCGCAAAGTGCTATTACGCATGACCAGCTGGGTGCATTACCTTTATCTCGATCAtt                    >  1:77267/1‑70 (MQ=255)
                                                    cATGTCTCGGTGATGCGCAAAGTGCTATTACGCATGACCAGCTGGGTGCATTACCTTTATCTCGATCAtt                    >  1:3698512/1‑70 (MQ=255)
                                                     aTGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTa                                     >  1:3891288/1‑52 (MQ=255)
                                                     aTGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTa                               >  1:407296/1‑58 (MQ=255)
                                                     aTGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGTTCATTga                  <  1:1162533/71‑1 (MQ=255)
                                                     aTGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGATCAtt                    >  1:3023694/1‑69 (MQ=255)
                                                     aTGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGATCAtt                    >  1:1513791/1‑69 (MQ=255)
                                                      tGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTgg                          <  1:3492791/62‑1 (MQ=255)
                                                      tGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGTTCATTgag                 <  1:1721879/71‑1 (MQ=255)
                                                      tGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGATCATTgag                 <  1:2476756/71‑1 (MQ=255)
                                                       gtctCGGTGATGCGCAAAGTGCTATTACGCATGACCAGCTGGGTGCATTACCTTTATCTCGATCAt                     >  1:2826972/4‑66 (MQ=255)
                                                       gTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGATCATTgagg                >  1:1719969/1‑71 (MQ=255)
                                                         ttCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCAt                                       >  1:3599276/1‑46 (MQ=255)
                                                         ttCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGATCATTgagggg              >  1:3113909/1‑71 (MQ=255)
                                                          tCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGATCAt                     >  1:2674656/1‑63 (MQ=255)
                                                          tCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGATCATTgagggg              <  1:2331410/70‑1 (MQ=255)
                                                          tCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGATCATTgagggg              >  1:1591226/1‑70 (MQ=255)
                                                          tCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGATCATTgagggg              >  1:1621007/1‑70 (MQ=255)
                                                          tCGGTGATGCGCAAAGTGCTATTACGCATGACCAGCTGGGTGCATTACCTTTAt                              <  1:2896902/54‑1 (MQ=255)
                                                            ggTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTTGATCATTgagggggag           <  1:1659192/71‑1 (MQ=255)
                                                            ggTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGATCATTgagggggag           <  1:2609564/71‑1 (MQ=255)
                                                            ggTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGATCATTgaggggga            <  1:3515525/70‑1 (MQ=255)
                                                                 tGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGATCATTGagggggaggggg       >  1:2541047/1‑70 (MQ=255)
                                                                 tGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGATCATTGagggggaggggg       >  1:3676318/1‑70 (MQ=255)
                                                                  gcgcAAAGTGCTATTACGCATGACCAGCTGGGTGCATTACCTTTAtct                            >  1:1282629/1‑46 (MQ=255)
                                                                    ggAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTa                               <  1:1134184/43‑1 (MQ=255)
                                                                     gAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGTTCATTGAGGGGGAGGGGGGAGAt  <  1:965757/71‑1 (MQ=255)
                                                                     gAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGATCATTgagg                <  1:3503709/57‑1 (MQ=255)
                                                                     |                                                                      
CTTACCCGACGGCATCTACGCCCAGGTGGCGGTTTACTCCGACCATTTCAGCCATGTTTCGGTGATGCGGAAAGTGCTGCTAAGAATGACCAGCTGGATGCATTATCTTTATTTGGATCATTGAGGGGGAGGGGGGAGAT  >  minE/2571109‑2571248

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A