Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,002,200 T→G 100% M173R (ATG→AGG)  mecA2 → competence negative regulator MecA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,002,2000TG100.0% 180.2 / NA 52M173R (ATG→AGG) mecA2competence negative regulator MecA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (23/29);  total (23/29)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTTCTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATATGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACTATGCTAAAA  >  CP000730/1002065‑1002340
                                                                                                                                       |                                                                                                                                            
gTTCTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTg                                                                                                                                         <  1:332757/141‑1 (MQ=255)
gTTCTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTg                                                                                                                                         <  2:192538/141‑1 (MQ=255)
   cTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCGATAACTACAGAGTTTGAAGATTTGTTATATAGGGTGGATg                                                                                                                                      <  1:598172/141‑1 (MQ=255)
   cTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATg                                                                                                                                      >  2:475298/1‑141 (MQ=255)
           cAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTagtagt                                                                                                                              >  2:622222/1‑136 (MQ=255)
             aaaGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACttatta                                                                                                                            <  2:674508/141‑1 (MQ=255)
             aaaGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACttatta                                                                                                                            <  2:426115/141‑1 (MQ=255)
                   ttCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGc                                                                                                                      <  1:67656/141‑1 (MQ=255)
                   ttCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGc                                                                                                                      <  1:472270/141‑1 (MQ=255)
                    tCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCt                                                                                                                     <  1:760958/141‑1 (MQ=255)
                     cAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTg                                                                                                                    >  1:399712/1‑141 (MQ=255)
                       gctcgcaaaaaaACCAGAACACTCATTGTGAAAATGAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGTGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGta                                                                                                                  <  1:60846/135‑1 (MQ=255)
                          cGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGACGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTatat                                                                                                               >  2:536922/1‑141 (MQ=255)
                            tAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATAttt                                                                                                             <  2:127142/141‑1 (MQ=255)
                              aaaaTACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGTAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTg                                                                                                           <  2:277925/141‑1 (MQ=255)
                              aaaaTACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTg                                                                                                           >  2:659778/1‑141 (MQ=255)
                                 aTACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTgttt                                                                                                        >  1:26099/1‑138 (MQ=255)
                                 aTACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATa                                                                                                        >  1:474219/1‑141 (MQ=255)
                                 aTACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGATGTATATTTTGATa                                                                                                        >  1:26069/1‑141 (MQ=255)
                                 aTACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTAAAGCGAATGAGTATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATa                                                                                                        >  1:822039/1‑141 (MQ=255)
                                         aCAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGtt                                                                                                <  2:802611/141‑1 (MQ=255)
                                          cAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTg                                                                                               >  2:393649/1‑141 (MQ=255)
                                                      aaTTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCa                                                                                   <  2:436961/141‑1 (MQ=255)
                                                      aaTTTAACGATTTAGAAGATGTTATCAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCa                                                                                   <  1:218039/141‑1 (MQ=255)
                                                         ttAACGATTTAGAAGATGGTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTTATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTa                                                                                <  1:115702/141‑1 (MQ=255)
                                                          tAACGCTATAGAAGATGTTATTAATTATCTATATCATACCAATCTATTAACTACAGAGTTTTAATATTTGTTCTATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTaa                                                                               <  2:377900/141‑1 (MQ=255)
                                                           aaCGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTGGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTGGATAGTAATGTTGATCAAGAAGTCATTact                                                                              >  2:260971/1‑139 (MQ=255)
                                                              ggtttAGAAGATGGTATTAATGATGCATGTCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGAt                                                                           <  1:759446/139‑1 (MQ=255)
                                                              gATTTAGATGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGAt                                                                           <  1:439126/141‑1 (MQ=255)
                                                              gATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGAt                                                                           >  1:533160/1‑141 (MQ=255)
                                                                 ttAGAAGATGTCATTAATAACGGATATCATACAAATCCAATAACTACCGTGTTTGAAGTTTTGTTATATAGGGTTGTTGACACTTATTATTACGCTGTATATTTTTATAGTCATCTTTAGCGAGAAGTCATTAATGATAGt                                                                        <  2:10061/141‑1 (MQ=255)
                                                                  tAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGtt                                                                       <  2:399712/141‑1 (MQ=255)
                                                                      agaTGTTATTAATTATGCATATCATAGCAATCCAATGACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAg                                                                   <  2:66561/141‑1 (MQ=255)
                                                                        aTGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGATGTCATTAATGATCGTTAGAGTc                                                                 >  2:441674/1‑141 (MQ=255)
                                                                          gTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCaa                                                               <  2:744619/141‑1 (MQ=255)
                                                                            tattaATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGGTAGTTACAGTCAAtt                                                             <  1:622222/141‑1 (MQ=255)
                                                                            tattaATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATAAAGAGTTAATGATACTTATTATTATGCTGTATATTTTGATAGTCATGTTGTTCAAGAAGTCATTAATGATAGTTACAGTCAAtt                                                             >  2:163510/1‑141 (MQ=255)
                                                                               taattaTGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCt                                                          <  2:140739/141‑1 (MQ=255)
                                                                                    aTGCATATCATAGCAATCCCATAACTACCGAGCTTGAAGAGCTGTTATAAAGGGTTGATGGTACGTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAAt                                                     >  2:793174/1‑141 (MQ=255)
                                                                                             aTAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATATGCTTATc                                            >  2:321522/1‑141 (MQ=255)
                                                                                              tAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATcc                                           >  1:181411/1‑141 (MQ=255)
                                                                                                 cAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTAGATATTATTATGCTGTATATTTTGATAGTCAGGTTGATCGAGAAGTAATTAATGATAGTTACAGTGAATTGCTTGAATTTGGTAATCAAac                                        >  2:588436/1‑141 (MQ=255)
                                                                                                  aaTCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTCATGATAGTTACAGTCAATTGCTGGAATTTGCTTATCCAaca                                       >  1:188641/1‑141 (MQ=255)
                                                                                                    tCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAacaga                                     <  1:490814/141‑1 (MQ=255)
                                                                                                         tAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGacagaa                                <  2:662143/141‑1 (MQ=255)
                                                                                                                 gagTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGacagaaca                              >  2:182598/1‑135 (MQ=255)
                                                                                                                 gagTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGacagaaca                              <  1:182598/135‑1 (MQ=255)
                                                                                                                   gTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGttta                      <  1:7344/141‑1 (MQ=255)
                                                                                                                    tttGAAGATTTGTTATATAGGGTTGATTGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGtttat                     <  1:27056/141‑1 (MQ=255)
                                                                                                                      tGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGtttattt                   >  1:804696/1‑141 (MQ=255)
                                                                                                                         aGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTaaa                >  1:691022/1‑141 (MQ=255)
                                                                                                                         aGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTaaa                >  1:174869/1‑141 (MQ=255)
                                                                                                                                  atatagGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACTATGc       <  1:659778/141‑1 (MQ=255)
                                                                                                                                  atatagGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACTATGc       <  1:260304/141‑1 (MQ=255)
                                                                                                                                       tGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACTATGCTaaaa  <  2:496520/141‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                            
GTTCTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATATGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACTATGCTAAAA  >  CP000730/1002065‑1002340

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑