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
A9 F1 I1 R1 759 71.0 3673240 91.5% 3361014 104.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,565,464 C→A L129F (TTG→TTT)  yjiM ← putative 2‑hydroxyglutaryl‑CoA dehydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,565,4640CA100.0% 206.2 / NA 64L129F (TTG→TTT) yjiMputative 2‑hydroxyglutaryl‑CoA dehydratase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (28/36);  total (28/36)

TTTCAGCGCAATGGCATCGCGCAGAGCATCTTCGCTAATCTCGTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGCAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCGACCACCAGATCCGAAAAGTAGAAGTAGGGGCATTTATCGGTTTTGCCGAAGCCGT  >  NC_000913/4565332‑4565597
                                                                                                                                     |                                                                                                                                     
tttCAGCGCAATGGCATCGCGAAGAGCATCTTCGCTAA‑CTCGTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCa                                                                                                                                <  2:924253/139‑1 (MQ=255)
 ttCAGCGCAATGGCATCGCGCAGAGCATCTTCGCTAATCTCGTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCa                                                                                                                                >  1:941961/1‑139 (MQ=255)
     gcgcAATGGCATCGCGCAGAGCATCTTCGCTAATCTCGTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATcac                                                                                                                            <  2:941961/139‑1 (MQ=255)
          aTGGCATCGCGCAGAGCATCTTCGCTAATCTCGTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGaa                                                                                                                       <  1:1412985/139‑1 (MQ=255)
           tGGCATCGCGCAGAGCATCTTCGCTAATCTCGTGCCCAAAACGTTCTTCTACCGGTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAAc                                                                                                                      >  1:1029380/1‑139 (MQ=255)
                   cgcAGAGCATCTTCGCTAATCTCGTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTaa                                                                                                              >  1:673029/1‑139 (MQ=255)
                   cgcAGAGCATCTTCGCTAATCTCGTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTaa                                                                                                              >  1:641845/1‑139 (MQ=255)
                   cgcAGAGCATCTTCGCTAATCTCGTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTaa                                                                                                              >  1:1603822/1‑139 (MQ=255)
                      agagCATCTTCGCTAATCTCGTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACt                                                                                                           <  2:394878/139‑1 (MQ=255)
                          cATCTTCGCTAATCTCGTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGc                                                                                                       <  2:234236/139‑1 (MQ=255)
                           aTCTTCGCTAATCTCGTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCACAGCATCTCGGCTTT‑CCATAGCGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGcc                                                                                                      <  2:1174459/139‑1 (MQ=255)
                             cTTCGCTAATCTCGTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCAt                                                                                                    <  2:673029/139‑1 (MQ=255)
                             cTTCGCTAATCTCGTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCAt                                                                                                    <  1:427467/139‑1 (MQ=255)
                              ttCGCTAATCTCGTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATg                                                                                                   <  2:641845/139‑1 (MQ=255)
                              ttCGCTAATCTCGTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATg                                                                                                   <  2:1603822/139‑1 (MQ=255)
                                      tctcGTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGGTGTTGGGAAATTGCATCACATGaa                                                                                                                       <  1:1240611/111‑1 (MQ=255)
                                      tctcGTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCCTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATgga                                                                                                                       >  2:1240611/1‑109 (MQ=255)
                                          gTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGaa                                                                                                                       >  2:320842/1‑107 (MQ=255)
                                          gTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGaa                                                                                                                       <  1:320842/107‑1 (MQ=255)
                                           tGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAAt                                                                                                                                    <  1:833347/93‑1 (MQ=255)
                                           tGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCATTAACGCTGTTGGGAAAt                                                                                                                                    >  2:833347/1‑93 (MQ=255)
                                            gCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACAtttt                                                                                     >  1:1628752/1‑139 (MQ=255)
                                             cccAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGcc                                                                                                      <  1:559193/121‑1 (MQ=255)
                                             cccAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGcc                                                                                                      >  2:559193/1‑121 (MQ=255)
                                               cAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCtt                                                                                  >  2:1000609/1‑139 (MQ=255)
                                                  aaCGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTTCCCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTaaa                                                                                                             >  1:1178200/1‑110 (MQ=255)
                                                  aaCGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTTCCCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTaaa                                                                                                             <  2:1178200/110‑1 (MQ=255)
                                                        cttctACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTc                                                                         <  2:1468926/139‑1 (MQ=255)
                                                                           gcgcAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATcac                                                                                                                            <  2:1301484/69‑1 (MQ=255)
                                                                           gcgcAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATcac                                                                                                                            >  1:1301484/1‑69 (MQ=255)
                                                                             gcagcaTCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCGaccac                                                    <  2:1029380/139‑1 (MQ=255)
                                                                                     tcGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCGACCACCAGATCCg                                            <  2:1382696/139‑1 (MQ=255)
                                                                                     tcGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCGACCACCAGATCCg                                            <  1:770797/139‑1 (MQ=255)
                                                                                     tcGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCGACCACCAGATCCg                                            <  2:1476366/139‑1 (MQ=255)
                                                                                       ggCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGaa                                                                                                                       >  1:750604/1‑62 (MQ=255)
                                                                                       ggCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGaa                                                                                                                       <  2:750604/62‑1 (MQ=255)
                                                                                               cATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCg                                                         >  2:1538981/1‑117 (MQ=255)
                                                                                               cATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCg                                                         <  1:1538981/117‑1 (MQ=255)
                                                                                                      cacgcGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCa                                                                      <  2:1781500/97‑1 (MQ=255)
                                                                                                      cacgcGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCa                                                                      >  1:1781500/1‑97 (MQ=255)
                                                                                                      cacgcGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCg                                                         >  1:69495/1‑110 (MQ=255)
                                                                                                      cacgcGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCg                                                         <  2:69495/110‑1 (MQ=255)
                                                                                                       acgcGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCGACCACCAGATCCGAAAAGTAGAAGTAgggg                           >  1:460937/1‑139 (MQ=255)
                                                                                                       acgcGAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCGACCACCAGATCCGAAAAGTAGAAGTAgggg                           >  2:1496267/1‑139 (MQ=255)
                                                                                                       acgcGAGGCATCGTCCTTAACGCTGTTCGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCGACCACCAGATCCGAAAAGTAGAAGTAgggg                           <  1:1047487/139‑1 (MQ=255)
                                                                                                        cgcgAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCa                                                                                                     <  1:1269834/64‑1 (MQ=255)
                                                                                                        cgcgAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCa                                                                                                     >  2:1269834/1‑64 (MQ=255)
                                                                                                        cgcgAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCg                                                         <  1:516843/108‑1 (MQ=255)
                                                                                                        cgcgAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCg                                                         >  2:516843/1‑108 (MQ=255)
                                                                                                         gcgAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCa                                                                                             >  2:1345148/1‑71 (MQ=255)
                                                                                                         gcgAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCa                                                                                             <  1:1345148/71‑1 (MQ=255)
                                                                                                         gcgAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGtt                                                               <  1:1615394/101‑1 (MQ=255)
                                                                                                         gcgAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGtt                                                               >  2:1615394/1‑101 (MQ=255)
                                                                                                         gcgAGGCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCGACCACCAGATCCGAAAAGTAGAAGTAGGGGCa                         <  2:406421/139‑1 (MQ=255)
                                                                                                             ggCATCGTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCGACCACCAGATCCGAAAAGTAGAAGTAGGGGCATTTa                     <  2:1564290/139‑1 (MQ=255)
                                                                                                                   gTCCTTAACGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCGACCACCAGATCCGAAAAGTAGAAGTAGGGGCATTTATCGGtt               <  1:440489/139‑1 (MQ=255)
                                                                                                                         aaCGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATg                                                                                                   <  1:58014/49‑1 (MQ=255)
                                                                                                                         aaCGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATg                                                                                                   >  2:58014/1‑49 (MQ=255)
                                                                                                                           cGCTGTTGGGAAATTGCGTCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCg                                                         <  1:1052390/89‑1 (MQ=255)
                                                                                                                           cGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCg                                                         >  2:1052390/1‑89 (MQ=255)
                                                                                                                           cGCTGTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCGACCACCAGATCCGAAAAGTAGAAGTAGGGGCATTTATCGGTTTTGCCGaa       >  2:868059/1‑139 (MQ=255)
                                                                                                                               gTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAggt                                                                   >  2:1255846/1‑75 (MQ=255)
                                                                                                                               gTTGGGAAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAggt                                                                   <  1:1255846/75‑1 (MQ=255)
                                                                                                                                ttGGGAAATTGCATCACATGAACAGGCTTAAACTTCGCCATGTATTCATACATTTTCTTTTTGACGTCGCAGGTGGTTTCACCCACCAACAGATCCGAAAAGTAGAAGTAGGGGCATTTATCGGTTTTGACGAAGCCgc  >  1:170366/1‑138 (MQ=255)
                                                                                                                                     |                                                                                                                                     
TTTCAGCGCAATGGCATCGCGCAGAGCATCTTCGCTAATCTCGTGCCCAAAACGTTCTTCTACCGTTTTTTGCAAGCGCAGCATCTCGGCTTT‑CCATAACGCACGCGAGGCATCGTCCTTAACGCTGTTGGGCAATTGCATCACATGAACAGGCTTAAACTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCGCAGGTGGTTTCACCGACCACCAGATCCGAAAAGTAGAAGTAGGGGCATTTATCGGTTTTGCCGAAGCCGT  >  NC_000913/4565332‑4565597

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A