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 835,178 T→C 18.5% Y1212Y (TAT→TAC)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,1780TC18.5% 233.8 / 45.6 108Y1212Y (TAT→TAC) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (49/39);  new base C (15/5);  total (64/44)
Fisher's exact test for biased strand distribution p-value = 1.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 114 total aligned reads displayed.

CCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGAT  >  minE/835109‑835247
                                                                     |                                                                     
ccGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATg                                                                      >  1:2492454/1‑71 (MQ=255)
 cGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATgg                                                                     <  1:1564774/71‑1 (MQ=255)
     tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCAcc                                                                 <  1:2107802/71‑1 (MQ=255)
     tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCAcc                                                                 >  1:2510893/1‑71 (MQ=255)
       aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                                                >  1:752279/1‑70 (MQ=255)
       aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                                                               <  1:3905746/71‑1 (MQ=255)
        cGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTa                                                              <  1:3790188/71‑1 (MQ=255)
        cGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTa                                                              <  1:1450255/71‑1 (MQ=255)
          ccGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAgg                                                            <  1:1608918/71‑1 (MQ=255)
          ccGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAgg                                                            <  1:2113044/71‑1 (MQ=255)
          ccGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAgg                                                            <  1:1947147/71‑1 (MQ=255)
           cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGt                                                           >  1:2122653/1‑71 (MQ=255)
           cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGt                                                           >  1:1103851/1‑71 (MQ=255)
           cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGt                                                           >  1:3493589/1‑71 (MQ=255)
           cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGt                                                           >  1:2180020/1‑71 (MQ=255)
           cGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCgga                                                           >  1:2988429/1‑70 (MQ=255)
            gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGtt                                                          >  1:512370/1‑71 (MQ=255)
            gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGt                                                           >  1:879483/1‑70 (MQ=255)
             aaaCCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAgg                                                            >  1:1418749/1‑68 (MQ=255)
             aaaCCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACAGCTTTAACTACTATGGCACCGTAGGTTc                                                         >  1:850334/1‑71 (MQ=255)
             aaaCCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATc                                                         <  1:1117108/71‑1 (MQ=255)
              aaCCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTc                                                         >  1:538695/1‑70 (MQ=255)
               aCCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTa                                                       <  1:2975098/71‑1 (MQ=255)
                ccGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTaa                                                      >  1:524933/1‑71 (MQ=255)
                ccGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGACTTTAACTACTATGGCACCGTAGGTTCTaa                                                      <  1:2054333/71‑1 (MQ=255)
                   aCGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGaa                                                      >  1:821054/1‑68 (MQ=255)
                   aCGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAAcc                                                    <  1:1736336/70‑1 (MQ=255)
                   aCGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcg                                                   >  1:1386857/1‑71 (MQ=255)
                    cGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACcgc                                                  >  1:1024265/1‑71 (MQ=255)
                    cGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgc                                                  >  1:1413148/1‑71 (MQ=255)
                    cGCATATGATAGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCAACGTAGGTTCTAACcgc                                                  >  1:2120364/1‑71 (MQ=255)
                       atatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCGCCGTAGGTTCTAACCGCGAt                                               <  1:3111744/71‑1 (MQ=255)
                        tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGAt                                               >  1:2326822/1‑70 (MQ=255)
                         atGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGAt                                               >  1:2767866/1‑69 (MQ=255)
                          tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAg                                            >  1:2430583/1‑71 (MQ=255)
                          tGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGtt                                                          >  1:1163839/1‑57 (MQ=255)
                          tGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAg                                            >  1:2385409/1‑71 (MQ=255)
                          tGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAg                                            >  1:1928400/1‑71 (MQ=255)
                          tGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAg                                            >  1:3775995/1‑71 (MQ=255)
                            attggcggtTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGCTCGAACCGCGATGAGtt                                          >  1:917970/4‑71 (MQ=255)
                             tCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGttt                                         <  1:2406389/71‑1 (MQ=255)
                               ggcggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGa                                             >  1:1534694/1‑65 (MQ=255)
                               ggcggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgt                                       <  1:1211359/71‑1 (MQ=255)
                               ggcggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttg                                        <  1:2815226/70‑1 (MQ=255)
                                gcggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGAt                                               <  1:397028/62‑1 (MQ=255)
                                 cggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                     <  1:3315226/71‑1 (MQ=255)
                                   gcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                     >  1:1368259/1‑69 (MQ=255)
                                    cTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAAcc                                                    <  1:2392088/53‑1 (MQ=255)
                                    cTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcg                                                   <  1:2689045/54‑1 (MQ=255)
                                     tATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGt                                 >  1:577755/1‑71 (MQ=255)
                                      aTGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgcg                                                 >  1:2537532/1‑54 (MQ=255)
                                         cccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGAt                                               >  1:3937580/1‑53 (MQ=255)
                                         cccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTtgttgt                                    <  1:3111698/64‑1 (MQ=255)
                                          ccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTc                                                         <  1:3658235/42‑1 (MQ=255)
                                          ccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGc                               >  1:1738706/1‑68 (MQ=255)
                                           cATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                   <  1:1549713/63‑1 (MQ=255)
                                            aTCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTaa                                                      >  1:730364/1‑43 (MQ=255)
                                            aTCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTtgttgt                                    <  1:3531113/61‑1 (MQ=255)
                                            aTCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGt                             >  1:470160/1‑68 (MQ=255)
                                              cTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAg                                  >  1:1887257/1‑61 (MQ=255)
                                               tGGCATACGGCTTTAACTACTATGGCACCGTAGGtt                                                          >  1:1635951/1‑36 (MQ=255)
                                               tGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTtgttgt                                    >  1:175682/1‑58 (MQ=255)
                                                ggCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATg                                              <  1:1965582/47‑1 (MQ=255)
                                                 gCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCg                              >  1:1782375/1‑62 (MQ=255)
                                                 gCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATg                       <  1:3848771/69‑1 (MQ=255)
                                                   aTACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAg                                  >  1:285395/1‑56 (MQ=255)
                                                    tACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                     <  1:1845858/52‑1 (MQ=255)
                                                    tACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaagaa                  >  1:3157522/1‑71 (MQ=255)
                                                     aCGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaagaa                  >  1:2662020/1‑70 (MQ=255)
                                                      cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAAc                 <  1:1441248/70‑1 (MQ=255)
                                                      cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                >  1:3578172/1‑71 (MQ=255)
                                                       ggCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                >  1:1272169/1‑70 (MQ=255)
                                                       ggCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAAcgt               >  1:1695585/1‑69 (MQ=255)
                                                         cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTtgttgt                                    <  1:2013526/48‑1 (MQ=255)
                                                         cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt              >  1:3558716/1‑70 (MQ=255)
                                                         cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt              >  1:2849592/1‑70 (MQ=255)
                                                         cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTg             <  1:3580214/71‑1 (MQ=255)
                                                         cTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGtta             <  1:297796/71‑2 (MQ=255)
                                                           ttAACTACTATGGCACCGTAGGTTCTAACCGCGATGa                                             >  1:1594689/1‑37 (MQ=255)
                                                           ttAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGt                                 >  1:1880774/1‑49 (MQ=255)
                                                           ttAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc           >  1:2248875/1‑71 (MQ=255)
                                                           ttAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc           >  1:110190/1‑71 (MQ=255)
                                                           ttAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc           >  1:2657265/1‑71 (MQ=255)
                                                           atAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                   >  1:314686/2‑47 (MQ=255)
                                                             aaCTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTg         >  1:48316/1‑71 (MQ=255)
                                                              actactACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAAcg                <  1:1522885/63‑2 (MQ=255)
                                                              actactACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTgg        >  1:1627332/1‑71 (MQ=255)
                                                              actactACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTgg        <  1:914913/71‑1 (MQ=255)
                                                                  ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa     <  1:3220800/70‑1 (MQ=255)
                                                                  ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa     <  1:2382585/70‑1 (MQ=255)
                                                                  ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa     <  1:1907475/70‑1 (MQ=255)
                                                                  ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa     <  1:3456589/70‑1 (MQ=255)
                                                                  ctaCGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTggctg     <  1:1429012/70‑4 (MQ=255)
                                                                  ctaCGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTggctg     >  1:2086464/1‑67 (MQ=255)
                                                                     tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAAc                 >  1:3636905/1‑55 (MQ=255)
                                                                     tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGa            >  1:3271910/1‑60 (MQ=255)
                                                                     tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGa            >  1:543449/1‑60 (MQ=255)
                                                                     tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGa            >  1:1677448/1‑60 (MQ=255)
                                                                     tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGa            >  1:2879013/1‑60 (MQ=255)
                                                                     tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt  <  1:1095397/70‑1 (MQ=255)
                                                                     |                                                                     
CCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGAT  >  minE/835109‑835247

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