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
A7 F1 I2 R1 94 59.5 3027142 91.9% 2781943 108.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,393,110 T→C intergenic (‑69/+95) nuoM ← / ← nuoL NADH:ubiquinone oxidoreductase, membrane subunit M/NADH:ubiquinone oxidoreductase, membrane subunit L

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,393,1100TC100.0% 220.2 / NA 60intergenic (‑69/+95)nuoM/nuoLNADH:ubiquinone oxidoreductase, membrane subunit M/NADH:ubiquinone oxidoreductase, membrane subunit L
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (27/33);  total (27/33)

AGCGTTCGGTCTGCCAGCACAGGAAGCCGCCAATAAAGGGAATTAATATTAGCCAGGGTAGTAACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATTCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCAATCCCACAATCCTTAACTCAACGCAGTACCATCAACAGTGCCAG  >  NC_000913/2392975‑2393231
                                                                                                                                       |                                                                                                                         
aGCGTTCGGTCTGCCAGCACAGGAAGCCGCCAATAAAGGGAATTAATATTAGCCAGGGTAGTAACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATcctc                                                                                                                        >  2:1188466/1‑139 (MQ=255)
  cGTTCGGTCGGCCAGCACAGGAAGCCGCCAATAAAGGGAATTAATATTAGCCAGGGTAGTAACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCtt                                                                                                                      <  1:823500/139‑1 (MQ=255)
   gTTCGGTCTGCCAGCACAGGAAGCCGCCAATAAAGGGAATTAATATTAGCCAGGGTAGTAACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTc                                                                                                                     <  2:1453837/139‑1 (MQ=255)
     tCGGTCTGCCAGCACAGGAAGCCGCCAATAAAGGGAATTAATATTAGCCAGGGTAGTAACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCgg                                                                                                                   <  2:137018/139‑1 (MQ=255)
        gTCTGCCAGCACAGGAAGCCGCCAATAAAGGGAATTAATATTAGCCAGGGTAGTAACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACt                                                                                                                <  2:549516/139‑1 (MQ=255)
                       aaGCCGCCAATAAAGGGAATTAATATTAGCCAGGGTAGTAACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGa                                                                                                 >  1:54155/1‑139 (MQ=255)
                           cgccAATAAAGGGAATTAATATTAGCCAGGGTAGTAACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCa                                                                                             >  2:1111142/1‑139 (MQ=255)
                                    aGGGAATTAATATTAGCCAGGGTAGTAACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAgg                                                                                    <  2:1426069/139‑1 (MQ=255)
                                      ggAATTAATATTAGCCAGGGTAGTAACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAggcg                                                                                  >  1:353623/1‑139 (MQ=255)
                                              tatTAGCCAGGGTAGTAACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATcc                                                                          <  1:1188466/139‑1 (MQ=255)
                                                    ccAGGGTAGTAACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTa                                                                    <  1:1158253/139‑1 (MQ=255)
                                                      aGGGTAGTAACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTG‑CGGATGCACCGCGAAGGCGGCTTATCCGACCTACGt                                                                 <  2:1279056/139‑1 (MQ=255)
                                                        ggTAGTAACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCt                                                                     <  1:1090260/134‑1 (MQ=255)
                                                        ggTAGTAACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCt                                                                     >  2:1090260/1‑134 (MQ=255)
                                                        ggTAGTAACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGtt                                                                >  1:1168379/1‑139 (MQ=255)
                                                        ggTAGTAACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGtt                                                                >  1:1166038/1‑139 (MQ=255)
                                                             taACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGaa                                                                                      >  2:532099/1‑112 (MQ=255)
                                                             taACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGaa                                                                                      <  1:532099/112‑1 (MQ=255)
                                                                  tGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGt                                                                 <  2:1053445/128‑1 (MQ=255)
                                                                  tGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGt                                                                 >  1:1053445/1‑128 (MQ=255)
                                                                  tGGCGATCTTTATTCCTTATAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGcc                                                      >  2:835723/1‑139 (MQ=255)
                                                                   ggCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGccc                                                     >  1:569811/1‑139 (MQ=255)
                                                                    gCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTggggg                                                                                                           <  2:1501506/84‑1 (MQ=255)
                                                                    gCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTggggg                                                                                                           >  1:1501506/1‑84 (MQ=255)
                                                                        tCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAgggg                                                <  2:353623/139‑1 (MQ=255)
                                                                          tttATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCa                                              >  2:881975/1‑139 (MQ=255)
                                                                                ccTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCAATCCca                                        <  2:123755/139‑1 (MQ=255)
                                                                                ccTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCAATCCca                                        <  2:1168379/139‑1 (MQ=255)
                                                                                  ttGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCAATCCcaca                                      <  2:1166038/139‑1 (MQ=255)
                                                                                   tGTAAAAGTCCCGTCAGGGCCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGcc                                                      >  2:836186/1‑122 (MQ=255)
                                                                                   tGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTc                                                                                                                     >  1:69088/1‑59 (MQ=255)
                                                                                   tGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTc                                                                                                                     <  2:69088/59‑1 (MQ=255)
                                                                                   tGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAgt                                                                                                       <  2:336657/73‑1 (MQ=255)
                                                                                   tGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAgt                                                                                                       >  1:336657/1‑73 (MQ=255)
                                                                                   tGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTa                                                                    >  1:654727/1‑108 (MQ=255)
                                                                                   tGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTa                                                                    <  2:654727/108‑1 (MQ=255)
                                                                                   tGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGt                                                                 >  1:1029018/1‑111 (MQ=255)
                                                                                   tGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGt                                                                 <  2:1029018/111‑1 (MQ=255)
                                                                                   tGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGcc                                                      <  1:836186/122‑1 (MQ=255)
                                                                                   tGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCa                                              >  1:1310214/1‑130 (MQ=255)
                                                                                   tGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCa                                              <  2:1310214/130‑1 (MQ=255)
                                                                                   tGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCAATCCCACaa                                     >  1:120179/1‑139 (MQ=255)
                                                                                    gTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGCAGGCGGCTTATCCGACCTACGTTCTtat                                                           <  1:934897/116‑1 (MQ=255)
                                                                                    gTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACg                                                                  >  1:695252/1‑109 (MQ=255)
                                                                                    gTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACg                                                                  <  2:695252/109‑1 (MQ=255)
                                                                                    gTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTtat                                                           >  2:934897/1‑116 (MQ=255)
                                                                                           tCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGAc                                                                       <  1:1480188/97‑1 (MQ=255)
                                                                                           tCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGAc                                                                       >  2:1480188/1‑97 (MQ=255)
                                                                                               gTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCAATCCCACAATCCTTAACTCaa                         <  1:1504615/139‑1 (MQ=255)
                                                                                                   ggACCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCAATCCCACAATCCTTAACTCAACGCa                     <  1:835723/139‑1 (MQ=255)
                                                                                                     aCCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCAATCCCACAATCCTTAACTCa                          >  2:482620/1‑132 (MQ=255)
                                                                                                     aCCGGATTTTCAACGAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCAATCCCACAATCCTTAACTCa                          <  1:482620/132‑1 (MQ=255)
                                                                                                                   gAATTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCAATCCCACAATCCTTAACTCAACGCAGTACCATCAACAGTGc     >  1:1432891/1‑139 (MQ=255)
                                                                                                                    aaTTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCAATCCCACAATCCTTAACTCAACGCAGTACCATCAACAGTGcc    <  2:1432891/139‑1 (MQ=255)
                                                                                                                     aTTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATACACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCAATCCCACAATCCTTAACTCAACGCAGTACCATCAACAGt       >  2:666541/1‑135 (MQ=255)
                                                                                                                     aTTCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATACACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCAATCCCACAATCCTTAACTCAACGCAGTACCATCAACAGt       <  1:666541/135‑1 (MQ=255)
                                                                                                                      ttCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATc                                                                           <  2:1191479/66‑1 (MQ=255)
                                                                                                                      ttCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATc                                                                           >  1:1191479/1‑66 (MQ=255)
                                                                                                                      ttCTCACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCAATCCCACAATCCTTAACTCAACGCAGTACCATCAACAGTGCCAg  <  2:120179/139‑1 (MQ=255)
                                                                                                                        ctcACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCa                                              <  2:483198/93‑1 (MQ=255)
                                                                                                                        ctcACGACAGAAAATCCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCa                                              >  1:483198/1‑93 (MQ=255)
                                                                                                                                       |                                                                                                                         
AGCGTTCGGTCTGCCAGCACAGGAAGCCGCCAATAAAGGGAATTAATATTAGCCAGGGTAGTAACATGGCGATCTTTATTCCTTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCTCACGACAGAAAATTCTCTTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGGCGGCTTATCCGACCTACGTTCTTATATGCCCAGGGGCAATCCCACAATCCTTAACTCAACGCAGTACCATCAACAGTGCCAG  >  NC_000913/2392975‑2393231

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A