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 835,190 T→A 19.1% G1216G (GGT→GGA)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,1900TA19.1% 232.0 / 43.7 101G1216G (GGT→GGA) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (43/38);  new base A (14/5);  total (58/43)
Fisher's exact test for biased strand distribution p-value = 1.27e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

Only 100 of 111 total aligned reads displayed.

CGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATG  >  minE/835120‑835260
                                                                      |                                                                      
cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGt                                                                        >  1:1103851/1‑71 (MQ=255)
cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGt                                                                        >  1:2122653/1‑71 (MQ=255)
cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGt                                                                        >  1:2180020/1‑71 (MQ=255)
cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGt                                                                        >  1:3493589/1‑71 (MQ=255)
 gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGtt                                                                       >  1:512370/1‑71 (MQ=255)
 gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGt                                                                        >  1:879483/1‑70 (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)
             tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGAt                                                            >  1:2326822/1‑70 (MQ=255)
               tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAg                                                         >  1:2430583/1‑71 (MQ=255)
               tGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGtt                                                                       >  1:1163839/1‑57 (MQ=255)
               tGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAg                                                         >  1:2385409/1‑71 (MQ=255)
               tGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAg                                                         >  1:3775995/1‑71 (MQ=255)
               tGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAg                                                         >  1:2004842/1‑71 (MQ=255)
               tGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAg                                                         >  1:1928400/1‑71 (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)
                    ggcggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgt                                                    <  1:467046/71‑1 (MQ=255)
                    ggcggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttg                                                     <  1:2815226/70‑1 (MQ=255)
                     gcggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGAt                                                            <  1:397028/62‑1 (MQ=255)
                      cggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                                  <  1:3315226/71‑1 (MQ=255)
                        gcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGTTTCTAACCGCGATGAGtt                                                       <  1:2175920/64‑1 (MQ=255)
                        gcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                                  >  1:1368259/1‑69 (MQ=255)
                        gcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                                <  1:3072486/71‑1 (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)
                           aTGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTg                                             >  1:1307414/1‑71 (MQ=255)
                              cccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTtgttgt                                                 <  1:3111698/64‑1 (MQ=255)
                               ccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTc                                                                      <  1:3658235/42‑1 (MQ=255)
                               ccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGc                                            >  1:1738706/1‑68 (MQ=255)
                               ccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGc                                            >  1:642834/1‑68 (MQ=255)
                               ccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTa                                         <  1:1495627/71‑1 (MQ=255)
                                 aTCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTaa                                                                   >  1:730364/1‑43 (MQ=255)
                                 aTCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGt                                          >  1:470160/1‑68 (MQ=255)
                                   cTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAg                                               >  1:1887257/1‑61 (MQ=255)
                                    tGGCATACGGCTTTAACTACTATGGCACCGTAGGtt                                                                       >  1:1635951/1‑36 (MQ=255)
                                    tGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGt                                              >  1:179754/1‑61 (MQ=255)
                                     ggCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATg                                                           <  1:1965582/47‑1 (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)
                                            ggCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAAcgt                            >  1:1695585/1‑69 (MQ=255)
                                              cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                           >  1:3558716/1‑70 (MQ=255)
                                              cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                           >  1:2849592/1‑70 (MQ=255)
                                              cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTg                          <  1:1633377/71‑1 (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                        >  1:110190/1‑71 (MQ=255)
                                                ttAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc                        >  1:2657265/1‑71 (MQ=255)
                                                ttAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc                        >  1:2248875/1‑71 (MQ=255)
                                                atAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                                >  1:314686/2‑47 (MQ=255)
                                                 tAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACt                       >  1:3348933/1‑71 (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)
                                                    ctactaCGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTggc                    >  1:3641095/1‑70 (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                         >  1:3271910/1‑60 (MQ=255)
                                                          tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGa                         >  1:1677448/1‑60 (MQ=255)
                                                          tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGa                         >  1:2879013/1‑60 (MQ=255)
                                                          tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt               <  1:1095397/70‑1 (MQ=255)
                                                            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)
                                                                      |                                                                      
CGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATG  >  minE/835120‑835260

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