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 835,031 C→T 22.0% Y1163Y (TAC→TAT)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,0310CT22.0% 236.1 / 55.7 118Y1163Y (TAC→TAT) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (36/56);  new base T (11/15);  total (47/71)
Fisher's exact test for biased strand distribution p-value = 8.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 121 total aligned reads displayed.

CAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTGGTGGTATCCATAACT  >  minE/834962‑835101
                                                                     |                                                                      
cAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTAcc                                                                       <  1:3832943/71‑1 (MQ=255)
 gccAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCa                                                                      >  1:1251324/3‑71 (MQ=255)
  ccAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCAc                                                                     >  1:4609626/2‑71 (MQ=255)
    aaCGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCAcgc                                                                   >  1:906405/1‑71 (MQ=255)
    aaCGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCAcgc                                                                   >  1:1958381/1‑71 (MQ=255)
     aCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCAcgcc                                                                  >  1:3788152/1‑70 (MQ=255)
       ggTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCAcgcg                                                                  >  1:4350576/1‑69 (MQ=255)
        gTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAg                                                               <  1:1291937/71‑1 (MQ=255)
         tGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAgg                                                              <  1:859508/71‑1 (MQ=255)
           cgctGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGaa                                                            <  1:412202/69‑1 (MQ=255)
             ctGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACg                                                          >  1:447976/1‑71 (MQ=255)
              tGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTTCGGCAGGGATGACCATGATGTACCACGCGCAGGAACg                                                          >  1:4915988/1‑70 (MQ=255)
               gACTGCCCGTGCGGTTGTCAGGCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTa                                                        >  1:4388736/1‑71 (MQ=255)
               gACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTa                                                        >  1:2540680/1‑71 (MQ=255)
                    cccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGtt                                                   <  1:4116101/71‑1 (MQ=255)
                    cccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGt                                                    >  1:2246713/1‑70 (MQ=255)
                    cccGCGCGGTGGTCAACCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCAttat                                                    >  1:45183/1‑67 (MQ=255)
                     ccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGt                                                         <  1:3891855/64‑1 (MQ=255)
                     ccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGt                                                         <  1:3707454/64‑1 (MQ=255)
                     ccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGt                                                         <  1:1621651/64‑1 (MQ=255)
                       gTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTAt                                                       <  1:2908133/64‑1 (MQ=255)
                        tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGtt                                                   <  1:3040612/67‑1 (MQ=255)
                        tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGtt                                                   <  1:679706/67‑1 (MQ=255)
                        tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGtt                                                   <  1:2860641/67‑1 (MQ=255)
                         gCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcct                                              >  1:1216563/1‑71 (MQ=255)
                          cGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctg                                             >  1:3045363/1‑71 (MQ=255)
                          cGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctg                                             >  1:4223642/1‑71 (MQ=255)
                             ttGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctgcct                                          <  1:1044911/71‑1 (MQ=255)
                             ttGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctgcct                                          <  1:2602551/71‑1 (MQ=255)
                               gTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACg                                                          >  1:1033878/1‑53 (MQ=255)
                               gTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTgg                                        >  1:4585703/1‑71 (MQ=255)
                               gTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCa                                                                <  1:2518405/47‑1 (MQ=16)
                               gTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCa                                                                <  1:4638057/47‑1 (MQ=16)
                               gTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCa                                                                <  1:3277177/47‑1 (MQ=16)
                                tCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGtt                                                   <  1:745313/59‑1 (MQ=255)
                                tCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCAt                                                       <  1:3224699/55‑1 (MQ=255)
                                 cagccaacGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACgc                                                         >  1:5210683/1‑51 (MQ=16)
                                  agccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTc                                     >  1:168575/1‑71 (MQ=255)
                                  agccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTc                                     >  1:832669/1‑71 (MQ=255)
                                  agccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTc                                     >  1:839341/1‑71 (MQ=255)
                                  agccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTc                                     >  1:2082186/1‑71 (MQ=255)
                                   gccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTa                                                  <  1:4065311/57‑1 (MQ=255)
                                   gccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTa                                                  <  1:2997136/57‑1 (MQ=255)
                                   gccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTa                                                  <  1:5384197/57‑1 (MQ=255)
                                    ccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg                                   <  1:4492449/71‑1 (MQ=255)
                                    ccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg                                   <  1:641250/71‑1 (MQ=255)
                                    ccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGCTTCgg                                   <  1:2188890/71‑1 (MQ=255)
                                    ccaacGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTCgg                                   <  1:3500068/71‑1 (MQ=255)
                                      agcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGa                                  >  1:1111952/1‑70 (MQ=255)
                                      agcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGa                                  <  1:5320507/70‑1 (MQ=255)
                                      aacGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAgg                                                              <  1:442422/40‑1 (MQ=12)
                                      aacGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTCg                                    <  1:1771948/66‑1 (MQ=255)
                                      aacGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTCGGaa                                 <  1:4544682/69‑1 (MQ=255)
                                       acGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGaa                                                            >  1:4853511/2‑43 (MQ=12)
                                        cGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg                                   <  1:3043868/67‑1 (MQ=255)
                                        cGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg                                   <  1:2805172/67‑1 (MQ=255)
                                        cGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg                                   <  1:5510869/67‑1 (MQ=255)
                                         gtgtACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTCGGaagt                               >  1:540723/1‑68 (MQ=255)
                                          tgtTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGt                                                    <  1:4029514/48‑1 (MQ=255)
                                          tgtTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGt                                                    <  1:4901642/48‑1 (MQ=255)
                                            ttCCGGCAGGGATGACCATGATGTACCACGCGCAg                                                               >  1:5210523/1‑35 (MQ=255)
                                            ttCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGa                                  <  1:3109862/64‑1 (MQ=255)
                                              ccGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGaaa                                >  1:630580/1‑64 (MQ=255)
                                              ccGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTAccc                          >  1:5149989/1‑70 (MQ=255)
                                              ccGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTAccc                          >  1:1956105/1‑70 (MQ=255)
                                               cGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCaa                        <  1:100192/71‑1 (MQ=255)
                                               cGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCa                         <  1:2256105/70‑1 (MQ=255)
                                                  cAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAg                     <  1:5439251/71‑1 (MQ=255)
                                                   aGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCaa                        >  1:3655850/1‑67 (MQ=255)
                                                   aGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGc                    >  1:2105595/1‑71 (MQ=255)
                                                   aGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGc                    <  1:711814/71‑1 (MQ=255)
                                                   aGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGc                    <  1:2919289/71‑1 (MQ=255)
                                                   aGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGc                    >  1:5220430/1‑71 (MQ=255)
                                                   aGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGc                    <  1:3324322/71‑1 (MQ=255)
                                                    gggATGACCATGATGTACCACGCGCAGTAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCCACAGCg                   <  1:740230/71‑1 (MQ=255)
                                                    gggATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAGATTACCCAACAGCg                   <  1:1989126/71‑1 (MQ=255)
                                                    gggATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCg                   >  1:32498/1‑71 (MQ=255)
                                                       aTGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCgtgg                <  1:1870127/71‑1 (MQ=255)
                                                       aTGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCgtgg                <  1:4157222/71‑1 (MQ=255)
                                                        tGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTCGGaagt                               <  1:2520382/55‑3 (MQ=255)
                                                        tGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTCGGaagt                               <  1:5571842/55‑3 (MQ=255)
                                                        tGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTCGGaagt                               <  1:5560455/55‑3 (MQ=255)
                                                         gACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTCgg                                   <  1:3391191/50‑1 (MQ=255)
                                                         gACCATGATGTACCACGCGCAGGAACGTATCGTTAAcc                                               <  1:4424211/38‑1 (MQ=255)
                                                         gACCATGATGTACCACGCGCAGGAACGTATCGTTAAcc                                               <  1:4516214/38‑1 (MQ=255)
                                                         gACCATGATGTACCACGCGCAGGAACGTATCGTTAAcc                                               <  1:1715527/38‑1 (MQ=255)
                                                          aCCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTAc                            >  1:3980459/1‑56 (MQ=255)
                                                           ccATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTggtggt            <  1:3594538/71‑1 (MQ=255)
                                                              tgatgTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGa                                  <  1:5377771/46‑1 (MQ=255)
                                                              tgatgTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGtggtgg             >  1:3078849/1‑67 (MQ=255)
                                                              tgatgTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTGGTGGTATc         >  1:4629983/1‑71 (MQ=255)
                                                               gatgTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTggtggt            <  1:5001685/67‑1 (MQ=255)
                                                                atgTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTGGTGGTATcc        <  1:4719251/70‑1 (MQ=255)
                                                                atgTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTGGTGGTATCCa       <  1:2565994/71‑1 (MQ=255)
                                                                 tgTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTGGTGGTATCCAt      <  1:755176/71‑1 (MQ=255)
                                                                 tgTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTGGTGGTATCCAt      <  1:1066530/71‑1 (MQ=255)
                                                                 tgTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTGGTGGTATCCAt      <  1:2338144/71‑1 (MQ=255)
                                                                  gTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTGGTGGTATCCAt      >  1:1364143/1‑70 (MQ=255)
                                                                   tACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTGGTGGTATCCATaa    >  1:4669266/1‑71 (MQ=255)
                                                                     ccACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTGGTGGTATCCATAACt  <  1:1293248/71‑1 (MQ=255)
                                                                     |                                                                      
CAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTGGTGGTATCCATAACT  >  minE/834962‑835101

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