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 835,208 T→C 15.3% F1222F (TTT→TTC)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,2080TC15.3% 201.9 / 27.1 85F1222F (TTT→TTC) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (37/35);  new base C (9/4);  total (46/39)
Fisher's exact test for biased strand distribution p-value = 3.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.58e-01

Only 100 of 103 total aligned reads displayed.

TCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG  >  minE/835138‑835278
                                                                      |                                                                      
tCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGttt                                                                        <  1:2406389/71‑1 (MQ=255)
  ggcggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgt                                                                      <  1:1211359/71‑1 (MQ=255)
  ggcggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgt                                                                      <  1:467046/71‑1 (MQ=255)
  ggcggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttg                                                                       <  1:2815226/70‑1 (MQ=255)
    cggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                                                    <  1:3315226/71‑1 (MQ=255)
      gcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                                                    >  1:1368259/1‑69 (MQ=255)
      gcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                                                  <  1:3072486/71‑1 (MQ=255)
        tATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGt                                                                >  1:577755/1‑71 (MQ=255)
         aTGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTg                                                               >  1:1307414/1‑71 (MQ=255)
            cccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTtgttgt                                                                   <  1:3111698/64‑1 (MQ=255)
             ccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGc                                                              >  1:642834/1‑68 (MQ=255)
             ccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGc                                                              >  1:1738706/1‑68 (MQ=255)
             ccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTa                                                           <  1:1495627/71‑1 (MQ=255)
              cATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                                                  <  1:1549713/63‑1 (MQ=255)
               aTCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTtgttgt                                                                   <  1:3531113/61‑1 (MQ=255)
               aTCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGt                                                            >  1:470160/1‑68 (MQ=255)
                 cTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAg                                                                 >  1:1887257/1‑61 (MQ=255)
                  tGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTtgttgt                                                                   >  1:175682/1‑58 (MQ=255)
                  tGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGt                                                                >  1:179754/1‑61 (MQ=255)
                    gCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                                                    <  1:2804415/55‑1 (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)
                       tACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaaga                                                  >  1:2413535/1‑70 (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                                             >  1:2849592/1‑70 (MQ=255)
                            cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                                             >  1:3558716/1‑70 (MQ=255)
                            cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTg                                            <  1:3580214/71‑1 (MQ=255)
                            cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTg                                            <  1:1633377/71‑1 (MQ=255)
                            cTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGtta                                            <  1:297796/71‑2 (MQ=255)
                              ttAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGt                                                                >  1:1880774/1‑49 (MQ=255)
                              ttAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc                                          >  1:2657265/1‑71 (MQ=255)
                              ttAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc                                          >  1:110190/1‑71 (MQ=255)
                              ttAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc                                          >  1:2248875/1‑71 (MQ=255)
                              atAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                                                  >  1:314686/2‑47 (MQ=255)
                                aaCTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTg                                        >  1:48316/1‑71 (MQ=255)
                                 actactACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAAcg                                               <  1:1522885/63‑2 (MQ=255)
                                 actactACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTgg                                       <  1:914913/71‑1 (MQ=255)
                                 actactACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTgg                                       >  1:1627332/1‑71 (MQ=255)
                                  ctactaCGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTggc                                      >  1:3641095/1‑70 (MQ=255)
                                     ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                    <  1:2382585/70‑1 (MQ=255)
                                     ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                    <  1:3456589/70‑1 (MQ=255)
                                     ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                    <  1:3220800/70‑1 (MQ=255)
                                     ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                    <  1:1907475/70‑1 (MQ=255)
                                     ctaCGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTggctg                                    <  1:1429012/70‑4 (MQ=255)
                                     ctaCGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTggctg                                    >  1:2086464/1‑67 (MQ=255)
                                       acggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                                 >  1:2152391/3‑71 (MQ=255)
                                        tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAAc                                                >  1:3636905/1‑55 (MQ=255)
                                        tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGa                                           >  1:543449/1‑60 (MQ=255)
                                        tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGa                                           >  1:2879013/1‑60 (MQ=255)
                                        tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGa                                           >  1:1677448/1‑60 (MQ=255)
                                        tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGa                                           >  1:3271910/1‑60 (MQ=255)
                                        tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt                                 <  1:1095397/70‑1 (MQ=255)
                                          gCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATg                                                      >  1:3240278/1‑47 (MQ=255)
                                           cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGAt                                                       <  1:1714743/45‑1 (MQ=255)
                                             ccGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAGGAACATTGACTGGTTAGATGGCGaa                           <  1:487614/71‑1 (MQ=255)
                                             ccGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                                               <  1:3599427/51‑1 (MQ=255)
                                             ccGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGaa                           <  1:725893/71‑1 (MQ=255)
                                                tAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGc                        <  1:464788/71‑1 (MQ=255)
                                                   gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                      <  1:1175320/54‑1 (MQ=255)
                                                    ttCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaagaa                                                 <  1:1097543/42‑1 (MQ=255)
                                                    ttCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATg                    <  1:1214518/71‑1 (MQ=255)
                                                     tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                                >  1:1144809/1‑58 (MQ=255)
                                                       tAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                     >  1:82640/1‑67 (MQ=255)
                                                        aaCCGCGATGAGTTTGTTGTAGTGCGTAAGATgaaga                                                  >  1:417241/1‑37 (MQ=255)
                                                        aaCCGCGATGAGTTTGTTGTAGTGCGTAAGATgaaga                                                  >  1:2092632/1‑37 (MQ=255)
                                                        aaCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                     <  1:2957897/66‑1 (MQ=255)
                                                         aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                                             <  1:645685/41‑1 (MQ=255)
                                                         aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                                             <  1:1961004/41‑1 (MQ=255)
                                                         aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                                             <  1:701564/41‑1 (MQ=255)
                                                         aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                                >  1:2595832/1‑54 (MQ=255)
                                                         aCCGAGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                     >  1:2624426/1‑65 (MQ=255)
                                                          ccGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                     >  1:1615579/1‑64 (MQ=255)
                                                          ccGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAg               <  1:3194256/70‑1 (MQ=255)
                                                           cgcgATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTg                                        >  1:3157168/1‑44 (MQ=255)
                                                           cgcgATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGt             <  1:3802636/71‑1 (MQ=255)
                                                              gatgatTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACa          <  1:652433/71‑1 (MQ=255)
                                                              gATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa                            <  1:3853295/53‑1 (MQ=255)
                                                              gATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa                            <  1:370518/53‑1 (MQ=255)
                                                              gATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa                            <  1:3274004/53‑1 (MQ=255)
                                                               aTGAGTTTGTTGTAGTGTGTAAGATGAAGAACATTGACTg                                        <  1:251812/40‑1 (MQ=255)
                                                               aTGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAg         <  1:853548/71‑1 (MQ=255)
                                                                 gAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                      >  1:1693123/1‑40 (MQ=255)
                                                                 gAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                      >  1:1997888/1‑40 (MQ=255)
                                                                  aGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCaa                      >  1:3146941/1‑55 (MQ=255)
                                                                  aGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGga       <  1:1839570/70‑1 (MQ=255)
                                                                  aGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGga       <  1:3819905/70‑1 (MQ=255)
                                                                     ttgttgTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGgaga     >  1:2702740/1‑69 (MQ=255)
                                                                     ttgttgTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGgaga     >  1:780615/1‑69 (MQ=255)
                                                                      tgttgtAGTGCGTAAGATGAAGAACATTGACTGGtt                                     <  1:3509032/36‑1 (MQ=255)
                                                                      tgttgtAGTGCGTAAGATGAAGAACATTGACTGGtt                                     <  1:3228479/36‑1 (MQ=255)
                                                                      tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGaa                           >  1:3896716/1‑46 (MQ=255)
                                                                      tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCg  >  1:541158/1‑71 (MQ=255)
                                                                      |                                                                      
TCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG  >  minE/835138‑835278

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