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
A12 F56 I1 R1 165 53.8 2611523 96.4% 2517508 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 318,690 A→G S438P (TCA→CCA)  rclA ← reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913318,6900AG97.1% 236.3 / ‑2.4 70S438P (TCA→CCA) rclAreactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family
Reads supporting (aligned to +/- strand):  ref base A (2/0);  new base G (34/34);  total (36/34)
Fisher's exact test for biased strand distribution p-value = 4.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01

AAGAAGTTATAGAGTAACAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGAAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGCCCGGCATCCATCACCATTTTCA  >  NC_000913/318593‑318785
                                                                                                 |                                                                                               
aagaagTTATAGAGTAACAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGgaa                                                                                               <  2:153981/100‑1 (MQ=255)
 agaagTTATAGAGTAACAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGgaaa                                                                                              >  1:334251/1‑100 (MQ=255)
   aagTTATAGAGTAACAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTACTGGAAAt                                                                                             >  2:564565/1‑99 (MQ=255)
    agTTATAGAGTAACAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAg                                                                                           <  2:193670/100‑1 (MQ=255)
     gTTATAGAGTAACAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTTTGTTTTTTTTACTAATGGAAATAGa                                                                                          >  2:1157920/1‑100 (MQ=255)
      ttATAGAGTAACAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGAt                                                                                         >  2:383743/1‑100 (MQ=255)
      ttATAGAGTAACAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGAt                                                                                         >  2:385912/1‑100 (MQ=255)
      ttATAGAGTAACAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGAAAATAGAt                                                                                         >  1:311404/1‑100 (MQ=255)
       tataGAGTAACAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATc                                                                                        <  1:608197/100‑1 (MQ=255)
        ataGAGTAACAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCa                                                                                       <  1:167805/100‑1 (MQ=255)
         taGAGTAACAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCAt                                                                                      >  1:1280052/1‑100 (MQ=255)
           gagTAACAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTg                                                                                    <  1:51620/100‑1 (MQ=255)
            agTAACAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGa                                                                                   <  1:603724/100‑1 (MQ=255)
             gTAACAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAg                                                                                  <  2:391345/100‑1 (MQ=255)
              tAACAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGt                                                                                 <  2:469207/100‑1 (MQ=255)
              tAACAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGt                                                                                 <  1:941829/100‑1 (MQ=255)
                aCAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGa                                                                               >  1:53185/1‑100 (MQ=255)
                 cAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGAt                                                                              >  2:371358/1‑100 (MQ=255)
                  agagAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGAtt                                                                             <  1:1125796/100‑1 (MQ=255)
                   gagaATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTc                                                                            >  1:1247107/1‑100 (MQ=255)
                   gagaATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTc                                                                            <  1:93394/100‑1 (MQ=255)
                   gagaATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGAAAATAGATCATTGAGTGATTc                                                                            >  2:656941/1‑100 (MQ=255)
                      aaTTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCt                                                                         <  1:965750/100‑1 (MQ=255)
                            taaGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGCCTAATGGAAATAGATCATTGAGTGATTCGCTCATCGa                                                                   <  2:699806/100‑1 (MQ=255)
                             aaGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGAc                                                                  >  1:533785/1‑100 (MQ=255)
                               gATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACgg                                                                >  2:834472/1‑100 (MQ=255)
                               gATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACgg                                                                <  1:252726/100‑1 (MQ=255)
                               gATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACgg                                                                <  2:1093348/100‑1 (MQ=255)
                                aTTCTTTTCTCTGAGACGCAAGCATCTTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATGGAGTGATTCGCTCATCGACg                                                                 >  2:107126/1‑98 (MQ=255)
                                 ttCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGAt                                                              >  2:1280923/1‑100 (MQ=255)
                                  tCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATg                                                             >  1:1051749/1‑100 (MQ=255)
                                  tCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATg                                                             <  1:427875/100‑1 (MQ=255)
                                  tCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATg                                                             >  1:1051826/1‑100 (MQ=255)
                                     tttCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGt                                                          <  2:1247096/100‑1 (MQ=255)
                                      ttCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTa                                                         >  2:338829/1‑100 (MQ=255)
                                        ctctGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTaaa                                                       >  1:513769/1‑100 (MQ=255)
                                         tctGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAat                                                      <  2:1223078/100‑1 (MQ=255)
                                          atcagaCGCCAGAACAAATATTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAata                                                     >  1:1147013/4‑100 (MQ=37)
                                            gagaCGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATc                                                   >  2:1262096/1‑100 (MQ=255)
                                            gagaCGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATc                                                   <  1:979949/100‑1 (MQ=255)
                                            gagaCGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATc                                                   <  1:154559/100‑1 (MQ=255)
                                            cagaCGCAAGAACACATATTCTTGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGGGTGATTCGCTCATCGACGGATGAGTAAATATc                                                   >  2:216567/2‑100 (MQ=255)
                                              gaCGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTg                                                 <  2:485/100‑1 (MQ=255)
                                                cGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGAt                                               >  1:933390/1‑100 (MQ=255)
                                                  ccAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATcg                                             >  1:589919/1‑100 (MQ=255)
                                                   cAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATcgc                                            >  2:43331/1‑100 (MQ=255)
                                                       atatTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTaa                                        <  1:671180/100‑1 (MQ=255)
                                                         atTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAat                                       >  1:572844/1‑99 (MQ=255)
                                                            tGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGc                                   <  1:429177/100‑1 (MQ=255)
                                                            tGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGc                                   <  1:308044/100‑1 (MQ=255)
                                                             gTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCt                                  >  2:373155/1‑100 (MQ=255)
                                                                  ggCGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAg                             >  2:1022696/1‑100 (MQ=255)
                                                                    cGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCTTCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGc                           <  2:1190530/100‑1 (MQ=255)
                                                                    cGTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGc                           <  2:787899/100‑1 (MQ=255)
                                                                     gTCTGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCa                          <  2:828694/100‑1 (MQ=255)
                                                                        tGATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGcc                       <  1:1183381/100‑1 (MQ=255)
                                                                         gATTTTGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGccc                      >  1:451998/1‑100 (MQ=255)
                                                                           ttttGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGCCCgg                    <  2:1203077/100‑1 (MQ=255)
                                                                             ttGAGTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGCCCGGca                  >  1:263374/1‑100 (MQ=255)
                                                                                 gTTTATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGCCCGGcatcca              >  1:991289/1‑100 (MQ=255)
                                                                                    tATTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGCCCGGCATCCATCa           >  1:562556/1‑100 (MQ=255)
                                                                                     aTTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGCCCGGCATCCATCa           <  2:813610/99‑1 (MQ=255)
                                                                                     aTTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGCCCGGCATCCATCAc          <  2:390086/100‑1 (MQ=255)
                                                                                     aTTTGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGCCCGGCATCCATCAc          <  1:1224894/100‑1 (MQ=255)
                                                                                      tttGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGCCCGGCATCCATCAcc         >  2:1055495/1‑100 (MQ=255)
                                                                                      tttGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGCCCGGCATCCATCAcc         >  2:400299/1‑100 (MQ=255)
                                                                                      tttGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGCCCGGCATCCATCAcc         <  2:912248/100‑1 (MQ=255)
                                                                                      nttGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGCCCGGCATCCATCAcc         >  1:598084/2‑100 (MQ=255)
                                                                                       ttGACTAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGCCCGGCATCCATCACCa        <  1:338832/100‑1 (MQ=255)
                                                                                            tAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGCCCGGCATCCATCACCATTTTc   >  2:367583/1‑100 (MQ=255)
                                                                                            tAATGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGCCCGGCATCCATCACCATTTTc   >  1:103946/1‑100 (MQ=255)
                                                                                             aaTGGAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGCCCGGCATCCATCACCATTTTCa  <  1:643669/100‑1 (MQ=255)
                                                                                                 |                                                                                               
AAGAAGTTATAGAGTAACAGAGAATTAATAAGATTCTTTTCTCTGAGACGCCAGAATATTTGTTCTGGCGTCTGATTTTGAGTTTATTTGACTAATGAAAATAGATCATTGAGTGATTCGCTCATCGACGGATGAGTAAATATCTGATCGCGTAATATGCTATAAGGCAGCCCGGCATCCATCACCATTTTCA  >  NC_000913/318593‑318785

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A