Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,147,479 G→A *114* (TAG→TAA) 
T280I (ACT→ATT) 		 frwD →
yijO ←		 putative enzyme IIB component of PTS
AraC family putative transcriptional activator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,147,4790GA100.0% 191.5 / NA 60*114* (TAG→TAA) 
T280I (ACT→ATT) 		frwD
yijO		putative enzyme IIB component of PTS
AraC family putative transcriptional activator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (28/32);  total (28/32)

TGCCGAGCGATTTGAACATTGCCGCTATGTGCAATGCAGCATCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAGTCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCACTTCTTTTACCTTC  >  NC_000913/4147347‑4147613
                                                                                                                                    |                                                                                                                                      
tGCCGAGCGATTTGAACATTGCCGCTATGTGCAATGCAGCATCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGtt                                                                                                                                  >  1:640832/1‑139 (MQ=255)
         aTTTGAACATTGCCGCTATGTGCAATGCAGCATCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCa                                                                                                                         <  2:322371/139‑1 (MQ=255)
               aCATTGCCGCTATGTGCAATGCAGCATCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGc                                                                                                                   <  2:1087685/139‑1 (MQ=255)
                 aTTGCCGCTATGTGCAATGCAGCATCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCtg                                                                                                                 <  2:1431836/139‑1 (MQ=255)
                   tGCCGCTATGTGCAATGCAGCATCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCtgtg                                                                                                               >  1:213626/1‑139 (MQ=255)
                    gCCGCTATGTGCAATGCAGCATCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTgg                                                                                                              >  2:1481926/1‑139 (MQ=255)
                      cGCTATGTGCAATGCAGCATCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTa                                                                                                            <  1:561142/139‑1 (MQ=255)
                        cTATGTGCAATGCAGCATCTACGCATTCCTGCGTGAGTCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACt                                                                                                          >  2:919240/1‑139 (MQ=255)
                           tgtgCAATGCAGCATCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGcc                                                                                                       <  2:213626/139‑1 (MQ=255)
                                     agcaTCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTGTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTc                                                                                             >  1:1445055/1‑139 (MQ=255)
                                                  tCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGc                                                                                                        >  2:623286/1‑115 (MQ=255)
                                                  tCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGc                                                                                                        <  1:623286/115‑1 (MQ=255)
                                                   ccTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGtt                                                                               >  2:503852/1‑139 (MQ=255)
                                                   ccTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGtt                                                                               >  1:159792/1‑139 (MQ=255)
                                                    cTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGtt                                                                                                                                  <  1:1184788/87‑1 (MQ=255)
                                                    cTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGtt                                                                                                                                  >  2:1184788/1‑87 (MQ=255)
                                                    cTGCGTGAGCCGCAGCGGG‑AATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTCATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCg                                                                             <  1:925042/139‑1 (MQ=255)
                                                     tGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTg                                                                                                                            >  2:574301/1‑92 (MQ=255)
                                                     tGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTg                                                                                                                            <  1:574301/92‑1 (MQ=255)
                                                       cGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGgt                                                                           >  1:289080/1‑139 (MQ=255)
                                                           aGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCa                                                                                                                         >  2:1503532/1‑89 (MQ=255)
                                                           aGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCa                                                                                                                         <  1:1503532/89‑1 (MQ=255)
                                                           aGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGttt                                                                       <  2:640832/139‑1 (MQ=255)
                                                            gCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGtt                                                                               >  1:1377728/1‑130 (MQ=255)
                                                            gCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGtt                                                                               <  2:1377728/130‑1 (MQ=255)
                                                            gCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGtttt                                                                      >  2:1439668/1‑139 (MQ=255)
                                                            gCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCAACTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGtttt                                                                      >  1:619310/1‑139 (MQ=255)
                                                                   cGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGaaa                                                               <  1:754415/139‑1 (MQ=255)
                                                                        aaTGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGAc                                                          <  2:1100596/139‑1 (MQ=255)
                                                                         aTGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACg                                                         <  2:686013/139‑1 (MQ=255)
                                                                          tGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACgg                                                        >  2:552634/1‑139 (MQ=255)
                                                                            aGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCa                                                      <  2:459411/139‑1 (MQ=255)
                                                                               gcgGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTc                                                                              <  2:1201973/112‑1 (MQ=255)
                                                                               gcgGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTc                                                                              >  1:1201973/1‑112 (MQ=255)
                                                                                cgGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTgg                                                                                                                    <  1:976524/73‑1 (MQ=255)
                                                                                cgGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTgg                                                                                                                    >  2:976524/1‑73 (MQ=255)
                                                                                cgGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAag                                                  >  2:1413515/1‑139 (MQ=255)
                                                                                     cgcAAAGTGCTTTCTGCGCCGCAGCAAACGCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATAATCCGACGGCGAGCGTTCGGTGTTTTTACGAAATAGACGGc                                                       <  2:983540/129‑1 (MQ=255)
                                                                                     cgcAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGc                                                       >  1:983540/1‑129 (MQ=255)
                                                                                      gcAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTg                                            <  2:1445055/139‑1 (MQ=255)
                                                                                             gCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTgg                                                                                                                    >  1:53508/1‑60 (MQ=255)
                                                                                             gCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTgg                                                                                                                    <  2:53508/60‑1 (MQ=255)
                                                                                                     cgccgcAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCg                             <  2:159792/139‑1 (MQ=255)
                                                                                                        cgcAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAg                          >  2:1418418/1‑139 (MQ=255)
                                                                                                          cagcaAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTgg                                                                                                                    <  1:79598/47‑1 (MQ=255)
                                                                                                          cagcaAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTgg                                                                                                                    >  2:79598/1‑47 (MQ=255)
                                                                                                           agcaAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCg                       <  2:809670/139‑1 (MQ=255)
                                                                                                             caAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTg                     <  1:281042/139‑1 (MQ=255)
                                                                                                                    aTCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCAct              <  1:1192048/139‑1 (MQ=255)
                                                                                                                       ttATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCActtct           >  2:1484056/1‑139 (MQ=255)
                                                                                                                          ttCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCACTTCtttt        <  2:289080/139‑1 (MQ=255)
                                                                                                                          ttCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCACTTCtttt        <  2:1211362/139‑1 (MQ=255)
                                                                                                                               gAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGAc                                                          >  2:735257/1‑84 (MQ=255)
                                                                                                                               gAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGAc                                                          <  1:735257/84‑1 (MQ=255)
                                                                                                                               gAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTgcg                   <  2:1604778/123‑1 (MQ=255)
                                                                                                                               gAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTgcg                   >  1:1604778/1‑123 (MQ=255)
                                                                                                                               gAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCa                >  2:1214674/1‑126 (MQ=255)
                                                                                                                               gAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCa                <  1:1214674/126‑1 (MQ=255)
                                                                                                                               gAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCACTTCTTTTACCtt   >  2:83593/1‑139 (MQ=255)
                                                                                                                               gAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCACTTCTTTTACCtt   <  1:1413515/139‑1 (MQ=255)
                                                                                                                                agtaatCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCACTTCTTTTACCTTc  <  1:503852/139‑1 (MQ=255)
                                                                                                                                    |                                                                                                                                      
TGCCGAGCGATTTGAACATTGCCGCTATGTGCAATGCAGCATCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAGTCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCACTTCTTTTACCTTC  >  NC_000913/4147347‑4147613

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑