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 835,193 T→G 27.9% S1217S (TCT→TCG)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,1930TG27.9% 150.7 / 113.5 140S1217S (TCT→TCG) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (45/56);  new base G (22/17);  total (67/73)
Fisher's exact test for biased strand distribution p-value = 2.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.35e-01

Only 100 of 149 total aligned reads displayed.

AACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAC  >  minE/835123‑835262
                                                                      |                                                                     
aaCCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                                                                       <  1:5628827/71‑1 (MQ=255)
  ccaaCGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGaa                                                                     <  1:2363058/68‑1 (MQ=255)
  ccGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTaa                                                                     <  1:3133452/71‑1 (MQ=255)
     aCGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACcg                                                                  >  1:194914/1‑71 (MQ=255)
      cGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgc                                                                 <  1:3139153/71‑1 (MQ=255)
       gCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgc                                                                 >  1:1627846/1‑70 (MQ=255)
         atatGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGAt                                                              <  1:2074863/71‑1 (MQ=255)
          tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                                                                       <  1:2636473/61‑1 (MQ=255)
          tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                                                                       <  1:1760513/61‑1 (MQ=255)
          tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATg                                                             <  1:387810/71‑1 (MQ=255)
          tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATg                                                             <  1:5284471/71‑1 (MQ=255)
            tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATg                                                             <  1:1093244/69‑1 (MQ=255)
            tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATg                                                             <  1:1835323/69‑1 (MQ=255)
            tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGa                                                            >  1:3248356/1‑70 (MQ=255)
            tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAg                                                           >  1:4471661/1‑71 (MQ=255)
             gATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGt                                                          >  1:805842/1‑71 (MQ=255)
             gATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGt                                                          >  1:1260521/1‑71 (MQ=255)
             gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGt                                                          >  1:2967366/1‑71 (MQ=255)
               ttggcggtTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGttc                                                        <  1:4466787/69‑2 (MQ=255)
               ttggcggtTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGttc                                                        <  1:3090538/69‑2 (MQ=255)
                tggcggtTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGttca                                                       >  1:4320174/2‑69 (MQ=255)
                   cggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                                    <  1:3619986/71‑1 (MQ=255)
                      cTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                                  >  1:3173179/1‑70 (MQ=255)
                      cTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACAGCGATGAGttt                                                        >  1:4370012/1‑64 (MQ=255)
                        aTGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTATGTTCTAACcgcg                                                                <  1:3713206/54‑1 (MQ=255)
                        aTGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgcg                                                                <  1:324015/54‑1 (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)
                                    cATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaag                                   <  1:3865259/71‑1 (MQ=255)
                                       ggggCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAAc                                >  1:4667421/3‑71 (MQ=255)
                                        cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGttt                                                        >  1:1959672/1‑46 (MQ=255)
                                        cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGtt                                                         >  1:1204618/1‑45 (MQ=255)
                                        cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                                  >  1:5170029/1‑52 (MQ=255)
                                        cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                                  >  1:4306227/1‑52 (MQ=255)
                                        cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                                  >  1:787744/1‑52 (MQ=255)
                                        cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                               >  1:5614683/1‑71 (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)
                                           cTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGtta                            <  1:3280931/71‑2 (MQ=255)
                                            tttAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGtt                             <  1:2956660/69‑1 (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                                                    <  1:1114237/42‑1 (MQ=255)
                                                actactATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                                    <  1:1108825/42‑1 (MQ=255)
                                                actactATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAt                              >  1:3442705/1‑64 (MQ=255)
                                                actactATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACt                         <  1:5176581/69‑1 (MQ=255)
                                                actactATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTgg                       <  1:4961804/71‑1 (MQ=255)
                                                 ctactaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTgg                       <  1:4001945/70‑1 (MQ=255)
                                                 ctactaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                      <  1:105446/71‑1 (MQ=255)
                                                  tactaTGGCACCGTAGGTTCTAACCGCGATGAGTTtgttgt                                                   <  1:4172156/41‑1 (MQ=255)
                                                    ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                      >  1:5368718/1‑68 (MQ=255)
                                                      acggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                 >  1:256060/3‑71 (MQ=255)
                                                       tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaa                                    >  1:1035745/1‑51 (MQ=255)
                                                       tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaa                                    >  1:1552395/1‑51 (MQ=255)
                                                       tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaa                                    >  1:3205365/1‑51 (MQ=255)
                                                       tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                               <  1:5095584/56‑1 (MQ=255)
                                                       tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                >  1:1344664/1‑71 (MQ=255)
                                                       cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGttaa                           >  1:5650863/2‑58 (MQ=255)
                                                       cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGttaa                           >  1:2452135/2‑58 (MQ=255)
                                                       cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                 <  1:1590219/69‑1 (MQ=255)
                                                       cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                 <  1:4956914/69‑1 (MQ=255)
                                                       cggCACCGTCGGATCGAACCGCGATGAGCTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                 >  1:283218/2‑70 (MQ=255)
                                                         gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat              >  1:3678124/1‑69 (MQ=255)
                                                         gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat              >  1:227615/1‑69 (MQ=255)
                                                         gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat              >  1:2619988/1‑69 (MQ=255)
                                                         gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATga               >  1:5190126/1‑69 (MQ=255)
                                                         gCACCGTCGGATCGAACCGCGATGACTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat              <  1:733046/71‑3 (MQ=255)
                                                         gCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATgg               <  1:5209487/70‑1 (MQ=255)
                                                          cACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat              >  1:3810990/1‑68 (MQ=255)
                                                          cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGc                                              <  1:1586383/38‑1 (MQ=255)
                                                          cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGTAGAACATTGACTGGTTAGATGGCg             <  1:2297451/71‑1 (MQ=255)
                                                          cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAg                   >  1:1898385/1‑65 (MQ=255)
                                                          cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCg             <  1:2319062/71‑1 (MQ=255)
                                                             cGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGt                                            <  1:2258041/37‑1 (MQ=255)
                                                              gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGa                                        >  1:1300459/1‑40 (MQ=255)
                                                              gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGa                                        >  1:4806926/1‑40 (MQ=255)
                                                              gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGGAGAACATTGACTGGTTa                    >  1:2039359/1‑60 (MQ=255)
                                                              gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAgg         >  1:932341/1‑71 (MQ=255)
                                                               tAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                               >  1:3197425/1‑48 (MQ=255)
                                                                  gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                             <  1:30916/47‑1 (MQ=255)
                                                                  gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                    <  1:5485123/56‑1 (MQ=255)
                                                                  gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt     <  1:959522/71‑1 (MQ=255)
                                                                  gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt     <  1:4239680/71‑1 (MQ=255)
                                                                   ttCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa            <  1:1123275/63‑1 (MQ=255)
                                                                   ttCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa            <  1:3286952/63‑1 (MQ=255)
                                                                    tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGc              <  1:1346366/60‑1 (MQ=255)
                                                                    tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGc              <  1:4522556/60‑1 (MQ=255)
                                                                     cTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc  >  1:340032/1‑71 (MQ=255)
                                                                      tAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                    <  1:628252/52‑1 (MQ=255)
                                                                      tAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                    <  1:4870463/52‑1 (MQ=255)
                                                                      tAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc  >  1:4231039/1‑70 (MQ=255)
                                                                      |                                                                     
AACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAC  >  minE/835123‑835262

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