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 835,178 T→C 27.2% 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
*minE835,1780TC27.2% 187.1 / 83.5 125Y1212Y (TAT→TAC) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (40/51);  new base C (20/14);  total (60/65)
Fisher's exact test for biased strand distribution p-value = 1.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.26e-01

Only 100 of 136 total aligned reads displayed.

CCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATG  >  minE/835109‑835248
                                                                     |                                                                      
ccGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATg                                                                       >  1:636062/1‑71 (MQ=255)
  gTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGc                                                                     <  1:3519468/71‑1 (MQ=255)
  gTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGc                                                                     <  1:4671923/71‑1 (MQ=255)
     tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCGATCTGGCATACGGCTTTAACTACTATGGCAcc                                                                  >  1:2397428/1‑71 (MQ=255)
     tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCAcc                                                                  >  1:916686/1‑71 (MQ=255)
       tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                                                                >  1:1028244/4‑71 (MQ=255)
       tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                                                                >  1:3265087/4‑71 (MQ=255)
       tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                                                                >  1:1140659/4‑71 (MQ=255)
       aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                                                 <  1:4760013/70‑1 (MQ=255)
       aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                                                 <  1:3495520/70‑1 (MQ=255)
       aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                                                 >  1:5120562/1‑70 (MQ=255)
       aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                                                 >  1:261888/1‑70 (MQ=255)
       aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                                                                <  1:263755/71‑1 (MQ=255)
        gcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGtc                                                               >  1:1715357/3‑70 (MQ=255)
          ccGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                                                                <  1:2645374/68‑1 (MQ=255)
           cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGt                                                            >  1:188003/1‑71 (MQ=255)
            gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAg                                                              >  1:1201454/1‑68 (MQ=255)
            gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGtt                                                           >  1:936588/1‑71 (MQ=255)
            gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGtt                                                           <  1:2364718/71‑1 (MQ=255)
            gAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCggat                                                           >  1:1957960/1‑69 (MQ=255)
            gAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCggat                                                           >  1:1801658/1‑69 (MQ=255)
              aaCCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                                                         <  1:5628827/71‑1 (MQ=255)
              aaCCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATc                                                          >  1:2485470/1‑70 (MQ=255)
               aCCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATcga                                                        <  1:1155060/71‑3 (MQ=255)
                ccGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTaa                                                       <  1:3133452/71‑1 (MQ=255)
                   aCGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACcg                                                    >  1:194914/1‑71 (MQ=255)
                    cGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgc                                                   <  1:5627680/71‑1 (MQ=255)
                     gCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgc                                                   >  1:1627846/1‑70 (MQ=255)
                       atatGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGAt                                                <  1:2074863/71‑1 (MQ=255)
                       atatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGAt                                                <  1:3939814/71‑1 (MQ=255)
                       atatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGAt                                                <  1:1623867/71‑1 (MQ=255)
                        tatGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCGCCGtcg                                                              <  1:1800593/56‑3 (MQ=255)
                        tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATg                                               <  1:387810/71‑1 (MQ=255)
                         atGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                                                         <  1:3015777/60‑1 (MQ=255)
                          tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGAt                                                >  1:480016/1‑68 (MQ=255)
                          tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATg                                               <  1:1093244/69‑1 (MQ=255)
                          tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGa                                              <  1:3098752/70‑1 (MQ=255)
                          tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAg                                             >  1:4471661/1‑71 (MQ=255)
                          tGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAg                                             <  1:5188796/71‑1 (MQ=255)
                           gATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGt                                            >  1:1260521/1‑71 (MQ=255)
                           gATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGt                                            >  1:805842/1‑71 (MQ=255)
                           gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                                                 >  1:3029433/1‑50 (MQ=255)
                           gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                                                 >  1:3139929/1‑50 (MQ=255)
                           gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                                                 >  1:2255828/1‑50 (MQ=255)
                           gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGt                                            >  1:2967366/1‑71 (MQ=255)
                              tggcggtTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGttca                                         >  1:4320174/2‑69 (MQ=255)
                                gcggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                                                                <  1:2652078/46‑1 (MQ=255)
                                 cggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                      <  1:809850/71‑1 (MQ=255)
                                 cggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                      <  1:3619986/71‑1 (MQ=255)
                                    cTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                    >  1:3173179/1‑70 (MQ=255)
                                    cTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACAGCGATGAGttt                                          >  1:4370012/1‑64 (MQ=255)
                                     tATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGt                                  >  1:235901/1‑71 (MQ=255)
                                      aTGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTATGTTCTAACcgcg                                                  <  1:3713206/54‑1 (MQ=255)
                                      aTGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgcg                                                  <  1:324015/54‑1 (MQ=255)
                                       tGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttg                                         <  1:4504329/62‑1 (MQ=255)
                                         cccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                                                         <  1:2125127/44‑1 (MQ=255)
                                         cccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                                                         <  1:4788922/44‑1 (MQ=255)
                                         cccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTaa                                                       >  1:725216/1‑46 (MQ=255)
                                          ccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAg                                   >  1:4510044/1‑65 (MQ=255)
                                          ccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAg                                   >  1:4361515/1‑65 (MQ=255)
                                               tGGCATCCGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAg                                   >  1:731687/1‑60 (MQ=255)
                                               tGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                      >  1:3993820/1‑57 (MQ=255)
                                                  cATACGGCTTTAACTACTATGGCACCGTAGGTCCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaag                     <  1:3211259/71‑1 (MQ=255)
                                                    tACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                      <  1:4254182/52‑1 (MQ=255)
                                                     ggggCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAAc                  >  1:4667421/3‑71 (MQ=255)
                                                     aCGGCTATAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaagaa                   >  1:730620/1‑70 (MQ=255)
                                                      cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGttt                                          >  1:2608722/1‑46 (MQ=255)
                                                      cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGttt                                          >  1:1966182/1‑46 (MQ=255)
                                                      cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                    >  1:787744/1‑52 (MQ=255)
                                                      cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                    >  1:4306227/1‑52 (MQ=255)
                                                      cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                 <  1:442185/71‑1 (MQ=255)
                                                      cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                 <  1:5282743/71‑1 (MQ=255)
                                                      cGGCTTTAACTACTATGGCACCCTAGGTTCTAACCGCGa                                                 >  1:5509859/1‑39 (MQ=255)
                                                       ggCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAAcgt                <  1:2579900/71‑3 (MQ=255)
                                                        gCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt               <  1:2893467/71‑1 (MQ=255)
                                                         cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt               >  1:3862488/1‑70 (MQ=255)
                                                         cTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGtta              <  1:3280931/71‑2 (MQ=255)
                                                           ttAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGtt                                           <  1:4115027/40‑1 (MQ=255)
                                                             aaCTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACt           <  1:3100500/70‑1 (MQ=255)
                                                             aaCTACTACGGGACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATgaagaa                   >  1:5171552/1‑62 (MQ=255)
                                                             aaCTACTACGGCACCGTCGGATCGAACCGCGATGAGttc                                          >  1:1521123/1‑38 (MQ=25)
                                                             aaCTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATgaagaa                   >  1:3456343/1‑62 (MQ=255)
                                                              actactATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                      <  1:3178041/42‑1 (MQ=255)
                                                              actactATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                      <  1:1108825/42‑1 (MQ=255)
                                                              actactATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACt           <  1:5176581/69‑1 (MQ=255)
                                                               ctactaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt        <  1:105446/71‑1 (MQ=255)
                                                               ctactaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt        <  1:2812972/71‑1 (MQ=255)
                                                               ctactaCGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTggc        <  1:3275169/71‑2 (MQ=255)
                                                                tactaTGGCACCGTAGGTTCTAACCGCGATGAGTTtgttgt                                     <  1:4172156/41‑1 (MQ=255)
                                                                  ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt        >  1:4961987/1‑68 (MQ=255)
                                                                  ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt        >  1:5368718/1‑68 (MQ=255)
                                                                     tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaa                      >  1:1035745/1‑51 (MQ=255)
                                                                     tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaa                      >  1:1552395/1‑51 (MQ=255)
                                                                     tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                 <  1:5095584/56‑1 (MQ=255)
                                                                     tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa    <  1:5171278/69‑1 (MQ=255)
                                                                     tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa    <  1:1103606/69‑1 (MQ=255)
                                                                     tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa    <  1:1782557/69‑1 (MQ=255)
                                                                     tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa    <  1:1230388/69‑1 (MQ=255)
                                                                     tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg  >  1:5242741/1‑71 (MQ=255)
                                                                     tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg  >  1:1344664/1‑71 (MQ=255)
                                                                     |                                                                      
CCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATG  >  minE/835109‑835248

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