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
A107 F1 I1 R1 19 326.9 20855348 93.1% 19416328 75.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA REL606 3,145,986 C→G I41M (ATC→ATG)  rpoD → RNA polymerase sigma factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*REL6063,145,9860CG99.5% 1655.7 / ‑2.3 377I41M (ATC→ATG) rpoDRNA polymerase sigma factor
Reads supporting (aligned to +/- strand):  ref base C (0/2);  new base G (178/197);  total (178/199)
Fisher's exact test for biased strand distribution p-value = 5.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

Only 100 of 428 total aligned reads displayed.

AGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTG  >  REL606/3145913‑3146058
                                                                         |                                                                        
aGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGa                                                                        <  2:898978/76‑1 (MQ=255)
 ggAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGaa                                                                       <  2:9447770/76‑1 (MQ=255)
  gAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAg                                                                      <  1:469047/76‑1 (MQ=255)
  gAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAg                                                                      >  2:7418055/1‑76 (MQ=255)
   aGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGa                                                                     >  1:192228/1‑76 (MQ=255)
    gCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGAc                                                                    >  1:5164124/1‑76 (MQ=255)
    gCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGAc                                                                    >  1:6954130/1‑76 (MQ=255)
    gCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGAc                                                                    >  2:7849581/1‑76 (MQ=255)
     cAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGAca                                                                   >  2:8211593/1‑76 (MQ=255)
      aaGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGAcat                                                                  >  2:1804616/1‑76 (MQ=255)
      aaGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGAcat                                                                  <  1:4825318/76‑1 (MQ=255)
       aGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGAcatc                                                                 <  1:7840490/76‑1 (MQ=255)
        ggCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGAcatca                                                                >  1:8662012/1‑76 (MQ=255)
         gCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGAcatcat                                                               <  1:3505538/76‑1 (MQ=255)
         gCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGAcatcat                                                               <  1:5399110/76‑1 (MQ=255)
          cTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACatcatc                                                              <  2:6293797/76‑1 (MQ=255)
          cTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACatcatc                                                              >  2:4580021/1‑76 (MQ=255)
           tATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATcc                                                             >  2:6141027/1‑76 (MQ=255)
           tATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATcc                                                             >  2:1136916/1‑76 (MQ=255)
           tATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATcc                                                             <  1:94387/76‑1 (MQ=255)
           tATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATcc                                                             <  2:2217042/76‑1 (MQ=255)
           tATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATcc                                                             >  1:8970185/1‑76 (MQ=255)
           tATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATcc                                                             >  1:3746122/1‑76 (MQ=255)
            aTCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCa                                                            <  2:9717950/76‑1 (MQ=255)
             tCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCaa                                                           <  2:8788862/76‑1 (MQ=255)
              cTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCaaa                                                          <  2:4167377/76‑1 (MQ=255)
              cTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCaaa                                                          >  1:3010272/1‑76 (MQ=255)
               tGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAAt                                                         <  1:6449713/76‑1 (MQ=255)
               tGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAAt                                                         <  1:1351574/76‑1 (MQ=255)
                 aCCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGa                                                       >  1:5743227/1‑76 (MQ=255)
                  ccTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGAt                                                      >  2:7065101/1‑76 (MQ=255)
                  ccTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGAt                                                      >  1:5990409/1‑76 (MQ=255)
                  ccTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGAt                                                      >  2:1095559/1‑76 (MQ=255)
                  ccTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGAt                                                      <  1:9656194/76‑1 (MQ=255)
                   cTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATc                                                     >  2:7275354/1‑76 (MQ=255)
                   cTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATc                                                     >  1:1218648/1‑76 (MQ=255)
                   cTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATc                                                     <  1:4300846/76‑1 (MQ=255)
                    tATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCa                                                    <  2:9169666/76‑1 (MQ=255)
                    tATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCa                                                    >  1:2090064/1‑76 (MQ=255)
                      tGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAAc                                                  >  1:9905950/1‑76 (MQ=255)
                       gCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACg                                                 <  1:5616818/76‑1 (MQ=255)
                       gCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACg                                                 <  1:3172793/76‑1 (MQ=255)
                         cGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGAc                                               <  1:8447130/76‑1 (MQ=255)
                         cGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGAc                                               <  1:3303911/76‑1 (MQ=255)
                           aGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACAt                                             >  2:5536562/1‑76 (MQ=255)
                            ggTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATg                                            >  1:4092872/1‑76 (MQ=255)
                              tCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATggg                                          >  2:5455886/1‑76 (MQ=255)
                              tCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATggg                                          >  1:2751190/1‑76 (MQ=255)
                              tCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATggg                                          >  1:7570568/1‑76 (MQ=255)
                               cAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGc                                         <  1:6319623/76‑1 (MQ=255)
                                aaTGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCa                                        >  2:2491972/1‑76 (MQ=255)
                                 aTGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCAt                                       <  1:9103300/76‑1 (MQ=255)
                                  tGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCAtt                                      >  1:7119445/1‑76 (MQ=255)
                                  tGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCAtt                                      <  1:8190941/76‑1 (MQ=255)
                                   gACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGa                                                >  2:844759/1‑65 (MQ=255)
                                   gACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTc                                     <  2:8706641/76‑1 (MQ=255)
                                    aCCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCa                                    >  2:1277451/1‑76 (MQ=255)
                                    aCCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCa                                    >  2:6685310/1‑76 (MQ=255)
                                    aCCATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCa                                    <  1:4913299/76‑1 (MQ=255)
                                     ccATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAg                                   <  1:1663700/76‑1 (MQ=255)
                                     ccATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAg                                   <  2:4817921/76‑1 (MQ=255)
                                     ccATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAg                                   >  1:950871/1‑76 (MQ=255)
                                     ccATCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATACAg                                   <  2:4001138/76‑1 (MQ=255)
                                       aTCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGt                                 <  1:5004909/76‑1 (MQ=255)
                                        tCTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTg                                >  2:148086/1‑76 (MQ=255)
                                         cTGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGa                               >  1:2328690/1‑76 (MQ=255)
                                          tGCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGAt                              <  2:7668601/76‑1 (MQ=255)
                                           gCCGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATg                             <  2:337872/76‑1 (MQ=255)
                                            ccGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATgg                            <  2:7731233/76‑1 (MQ=255)
                                            ccGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATgg                            <  2:5661480/76‑1 (MQ=255)
                                             cGGAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGga                           >  2:6784370/1‑76 (MQ=255)
                                              ggAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGgaa                          >  1:2603899/1‑76 (MQ=255)
                                               gAAGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGgaag                         >  2:5327911/1‑76 (MQ=255)
                                                 aGATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGgaagaa                       >  2:8375960/1‑76 (MQ=255)
                                                  gATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGaagaag                      <  2:9300552/76‑1 (MQ=255)
                                                  gATATCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGaagaag                      <  2:5852089/76‑1 (MQ=255)
                                                   atatCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGc                     >  1:10360506/1‑76 (MQ=255)
                                                   atatCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGc                     <  2:446426/76‑1 (MQ=255)
                                                    tatCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCa                    >  1:7275293/1‑76 (MQ=255)
                                                     atCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCAc                   >  1:10049118/1‑76 (MQ=255)
                                                     atCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCAc                   >  2:10147972/1‑76 (MQ=255)
                                                     atCGTCGATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCAc                   <  2:7175274/76‑1 (MQ=255)
                                                      tcgtcgATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCAcc                  <  1:416619/76‑1 (MQ=255)
                                                      tcgtcgATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCAcc                  <  1:3886404/76‑1 (MQ=255)
                                                       cttcgAGTCAGATCAGAGGCAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAACCACCg                 <  2:6850567/74‑1 (MQ=255)
                                                       cgtcgATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCg                 <  2:3889413/76‑1 (MQ=255)
                                                       cgtcgATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCg                 >  2:2720258/1‑76 (MQ=255)
                                                          cgATTCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGAt              <  2:2270110/76‑1 (MQ=255)
                                                             ttCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGcc           >  1:8128326/1‑76 (MQ=255)
                                                             ttCAGATCAGATGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGcc           >  1:5289768/1‑76 (MQ=255)
                                                              tcagatgagaTGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCg          <  2:5053392/76‑1 (MQ=255)
                                                              tcagatcagaTGGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCg          <  1:676307/76‑1 (MQ=255)
                                                                agatcagatgGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCgat        <  2:8062573/76‑1 (MQ=255)
                                                                agatcagatgGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCgat        <  1:2895765/76‑1 (MQ=255)
                                                                  atcagatgGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCgatga      >  1:4594605/1‑76 (MQ=255)
                                                                  atcagaggGATGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCgatga      <  2:192228/76‑1 (MQ=255)
                                                                   tcagatgGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCgatgat     >  2:2969506/1‑76 (MQ=255)
                                                                   tcagatgGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCgatgat     <  1:7726761/76‑1 (MQ=255)
                                                                    cagatgGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATc    >  2:3550318/1‑76 (MQ=255)
                                                                      gatgGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTg  <  1:8817058/76‑1 (MQ=255)
                                                                         |                                                                        
AGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTG  >  REL606/3145913‑3146058

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A