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
A2 F999 I1 R1 226 132.7 9745491 85.7% 8351885 75.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,930,457 Δ1 bp coding (1515/1560 nt) kup → low affinity potassium transport system

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,930,4570C.98.4% 558.3 / 2.9 127coding (1515/1560 nt)kuplow affinity potassium transport system
Reads supporting (aligned to +/- strand):  ref base C (1/0);  major base . (61/63);  minor base A (2/0);  total (64/63)
Fisher's exact test for biased strand distribution p-value = 4.96e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

Only 100 of 128 total aligned reads displayed.

CGTGCAATCAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGTCGATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGTACAGATTGAACAA  >  NC_000913/3930386‑3930527
                                                                       |                                                                      
cgTGCAATCAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTc                                                                   >  2:1697654/1‑76 (MQ=255)
 gTGCAATCAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCt                                                                  >  1:707418/1‑76 (MQ=255)
 gTGCAATCAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCt                                                                  >  2:4029604/1‑76 (MQ=255)
  agCAATCAACCTCATTCCCTTTGCGCTGACGCATAACCTCAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTg                                                                 >  2:1441915/2‑76 (MQ=255)
     aaTCAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTa                                                              >  1:2327680/1‑76 (MQ=255)
     aaTCAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTa                                                              >  2:1890863/1‑76 (MQ=255)
     aaTCAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTa                                                              >  1:3496414/1‑76 (MQ=255)
     aaTCAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTa                                                              >  2:165621/1‑76 (MQ=255)
     aaTCAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTa                                                              >  1:590608/1‑76 (MQ=255)
      aTCAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTaa                                                             >  2:533003/1‑76 (MQ=255)
      aTCAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTaa                                                             >  1:206361/1‑76 (MQ=255)
      aTCAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGG‑GGATTCTCTTaa                                                             >  2:4328651/1‑76 (MQ=255)
       tCAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAAc                                                            <  1:3642111/76‑1 (MQ=255)
        cAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGGGGGT‑GATTCTGTTAAct                                                           <  2:4719429/76‑1 (MQ=255)
        cAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAAct                                                           >  1:36467/1‑76 (MQ=255)
        cAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAAct                                                           >  1:434828/1‑76 (MQ=255)
        cAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAAct                                                           >  2:2368599/1‑76 (MQ=255)
        cAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAAct                                                           >  1:1018397/1‑76 (MQ=255)
        cAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAAca                                                           <  2:4045689/76‑2 (MQ=255)
         aaCGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAActc                                                          >  1:33605/1‑76 (MQ=255)
         aaCGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAActc                                                          <  2:2243495/76‑1 (MQ=255)
          aCGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAActct                                                         <  1:214103/76‑1 (MQ=255)
          aCGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAActct                                                         >  2:2746193/1‑76 (MQ=255)
           cGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTg                                                        >  1:193907/1‑76 (MQ=255)
            gTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTgc                                                       <  1:1938839/76‑1 (MQ=255)
            gTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTgc                                                       >  2:3532547/1‑76 (MQ=255)
            gTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTgc                                                       <  1:4388478/76‑1 (MQ=255)
             tCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTgcg                                                      >  1:1248570/1‑76 (MQ=255)
             tCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTgcg                                                      <  2:3829998/76‑1 (MQ=255)
               aTTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCa                                                    <  2:2862380/76‑1 (MQ=255)
                ttCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGG‑‑‑GATTCTGTTAACTCTGCGCACCg                                                 <  2:1444280/76‑1 (MQ=255)
                tgcccGTTGCGCTGATGAATAACCTGAAACATAACAAGGTATTGCATGAGCGG‑‑‑GATTCTGTTAACTCTGCGCACCg                                                 <  2:1458297/74‑1 (MQ=255)
                 tCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCAcc                                                  >  1:4216167/1‑76 (MQ=255)
                 tCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCAcc                                                  <  1:780008/76‑1 (MQ=255)
                 tCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCAcc                                                  <  1:640984/76‑1 (MQ=255)
                  cccTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCg                                                 >  1:670477/1‑76 (MQ=255)
                  cccTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCg                                                 <  2:3814771/76‑1 (MQ=255)
                   ccTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGa                                                >  1:4465552/1‑76 (MQ=255)
                    cTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGaa                                               >  2:1392007/1‑76 (MQ=255)
                     tttGTGCTGATGCATAACCTTAAACATAACAAGGTATTGCGTGAGCGGGT‑GATTCTGTTACCTCTGCGCACCGAAg                                              <  1:4426150/76‑1 (MQ=255)
                       tGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGAc                                            <  1:1703611/76‑1 (MQ=255)
                       tGCGCTGATGCATAAACTTAAACATAACAAGGCATTGCATGAGCGGG‑AGATTCTGGTAACTCTGCGCACCGAAGAc                                            >  2:901707/1‑76 (MQ=255)
                       tGCGCGGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGAc                                            <  1:1414923/76‑1 (MQ=255)
                        gcgcTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACg                                           <  1:1591100/76‑1 (MQ=255)
                        gcgcTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACg                                           <  1:2752588/76‑1 (MQ=255)
                        gcgcTGATGCATAACCTTAAACATAACAAGGTACTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACg                                           >  2:1165427/1‑76 (MQ=255)
                          gcTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCt                                         <  1:4804104/76‑1 (MQ=255)
                           cTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTc                                        >  2:903370/1‑76 (MQ=255)
                            tGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTcc                                       <  1:4543642/76‑1 (MQ=255)
                            tGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTcc                                       >  2:3750641/1‑76 (MQ=255)
                             gATGCATAAGCTTAAACGTAGCGAGGTATTGCATGTGCGGGT‑GATTCTGTTAACTTTGCGCACCGAAGACGCTCCa                                      <  2:1358675/76‑1 (MQ=255)
                              aTGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCat                                     >  1:648494/1‑76 (MQ=255)
                                gCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCatat                                   <  2:4766817/76‑1 (MQ=255)
                                 cATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATg                                  <  1:4761671/76‑1 (MQ=255)
                                 cATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATg                                  >  1:4523323/1‑76 (MQ=255)
                                 cATAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATg                                  <  1:3485745/76‑1 (MQ=255)
                                  aTAGCCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGt                                 <  1:1908734/76‑1 (MQ=255)
                                  aTAACCTTAACCATAACAAGGTATTGCATGCGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGt                                 <  1:3016568/76‑1 (MQ=255)
                                  aTAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGt                                 >  2:103705/1‑76 (MQ=255)
                                  aTAACCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGt                                 >  2:504274/1‑76 (MQ=255)
                                    gaCCTTAAACATAACAAGGTATTGCGTGAGCGGGT‑GATTCTGTTAGCTCTGCGCCCCGAAGACGCTCCCTATGTcc                               <  2:3706218/75‑1 (MQ=255)
                                     aCCTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCa                              <  1:3224746/76‑1 (MQ=255)
                                      ccTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCAt                             >  2:2326790/1‑76 (MQ=255)
                                      ccTTAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCAt                             <  2:1746895/76‑1 (MQ=255)
                                        ttAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATaa                           <  1:3566278/76‑1 (MQ=255)
                                         tAAACATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAAc                          <  2:2063149/76‑1 (MQ=255)
                                         tAAACATAACAAGGGATTGCATGAGCGGG‑AGACTCGGTGAACTCTGCGCACAGAAGACGCTCCATAGTGCCATAAc                          >  1:1152523/1‑76 (MQ=255)
                                             cATAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAAcgtcc                      >  1:3382519/1‑76 (MQ=255)
                                             aaTAGCAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCGCCGAAGACGCTCCATATGTCCATAAcgtcc                      <  2:419279/75‑1 (MQ=255)
                                               tAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAAcgtccgt                    <  2:2832639/76‑1 (MQ=255)
                                               tAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAAcgtccgt                    >  1:3571208/1‑76 (MQ=255)
                                               tAACAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAAcgtccgt                    <  1:1474076/76‑1 (MQ=255)
                                                caCAAGGTATTGCATGAGCGGGT‑GATTCTGTTCACTCTGCGCACCGCAGACGCTCCCTATGTCCATAAcgtccgtc                   >  2:2707295/2‑76 (MQ=255)
                                                aaCAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAAcgtccgtc                   >  2:2664952/1‑76 (MQ=255)
                                                aaCAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAAcgtccgtc                   <  2:3571208/76‑1 (MQ=255)
                                                aaCAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAAcgtccgtc                   >  2:1263503/1‑76 (MQ=255)
                                                 aCAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCg                  <  1:3631423/76‑1 (MQ=255)
                                                 aCAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGAGCAACGAAGACGCTCCATATGTCCAGAACGTCCGTCg                  >  1:4552049/1‑76 (MQ=255)
                                                  cAAGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCgg                 <  1:4024902/76‑1 (MQ=255)
                                                  cAAGGAATTGCCTGAGCGGGT‑GATTCTGTTAATTCTGCGCACCGAAGACGCTCCATATTTCCATAACGTCCGTggg                 >  1:1502799/1‑76 (MQ=255)
                                                    aGGTATTGCATGTGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGt               <  2:3447293/76‑1 (MQ=255)
                                                    aGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGt               <  1:591145/76‑1 (MQ=255)
                                                    aGGTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGt               <  1:2720630/76‑1 (MQ=255)
                                                    aGGTATTGCAGTAGCGTGT‑GAGTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAAAGTCCGTCGGGt               <  1:2510175/76‑1 (MQ=255)
                                                      gTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGTAc             <  1:1842030/76‑1 (MQ=255)
                                                      gTATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGTAc             >  2:1623055/1‑76 (MQ=255)
                                                       tATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGTACa            <  1:4408284/76‑1 (MQ=255)
                                                       tATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGTACa            >  2:2612901/1‑76 (MQ=255)
                                                       tATTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCACAAAGTCCGTCGGGTAcc            >  2:4397159/1‑75 (MQ=255)
                                                        aTTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGTACAg           <  1:2215429/76‑1 (MQ=255)
                                                        aTTGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGTACAg           >  1:812109/1‑76 (MQ=255)
                                                          tGCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGTACAGAt         >  1:1243190/1‑76 (MQ=255)
                                                           gCATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGTACAGAtt        <  2:1978917/76‑1 (MQ=255)
                                                            cATGAGGGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGTACAGATTg       <  2:4255197/76‑1 (MQ=255)
                                                            cATGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGTACAGATTg       >  2:2861118/1‑76 (MQ=255)
                                                             aTGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGTACAGATTGa      <  1:416165/76‑1 (MQ=255)
                                                             aTGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGTACAGATTGa      >  2:4387101/1‑76 (MQ=255)
                                                             aTGAGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGTACAGATTGa      <  2:2449535/76‑1 (MQ=255)
                                                                aGCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGTACAGATTGaaca   >  1:1825607/1‑76 (MQ=255)
                                                                 gCGGGT‑GATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGTACAGATTGaacaa  <  2:908115/76‑1 (MQ=255)
                                                                       |                                                                      
CGTGCAATCAACGTCATTCCCTTTGCGCTGATGCATAACCTTAAACATAACAAGGTATTGCATGAGCGGGTCGATTCTGTTAACTCTGCGCACCGAAGACGCTCCATATGTCCATAACGTCCGTCGGGTACAGATTGAACAA  >  NC_000913/3930386‑3930527

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A