Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,502,141 C→A 100% A222D (GCC→GAC)  USA300HOU_2364 → AraC transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,502,1410CA100.0% 143.1 / ‑6.5 52A222D (GCC→GAC) USA300HOU_2364AraC transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base A (33/18);  total (34/18)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCATATTGTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGCCGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAGATAACGTATCACA  >  CP000730/2502008‑2502276
                                                                                                                                     |                                                                                                                                       
tCATATTGTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGttt                                                                                                                                   <  2:568446/140‑1 (MQ=255)
 cATATTGTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGtttt                                                                                                                                  >  1:78181/1‑140 (MQ=255)
  atatTGTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAGGTATTAAACTTGTTGACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTa                                                                                                                                 >  2:139954/1‑140 (MQ=255)
   tatTTTTCTAATCTTTTTTTTAGATATTTGAGTATTAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTaa                                                                                                                                <  2:709793/140‑1 (MQ=255)
     ttGTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACa                                                                                                                              <  1:144383/140‑1 (MQ=255)
       gTTCTAATCTTTTTTTTTTATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTTTTTCTTAATTGGACGGTTTTAACatt                                                                                                                            >  2:326425/1‑138 (MQ=255)
       gTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGt                                                                                                                            >  1:652369/1‑140 (MQ=255)
          cTAATCTTTTTTTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCAt                                                                                                                         <  1:263181/140‑1 (MQ=255)
          cTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCAt                                                                                                                         <  1:522363/140‑1 (MQ=255)
           tAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATa                                                                                                                        <  2:667312/140‑1 (MQ=255)
             aTCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACCGTCATCCa                                                                                                                      >  2:305154/1‑140 (MQ=255)
              tCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACaa                                                                                                                     >  2:63985/1‑140 (MQ=255)
                tttttGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAAt                                                                                                                   >  1:164710/1‑140 (MQ=255)
                 ttttGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAAtt                                                                                                                  >  1:43030/1‑140 (MQ=255)
                     gTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGGCATCAATTTATTACTTTCTAAAAAATATTCAGTTACAAATGTTTATGAATTGACCGGTTTTAAAAGGAATCCAAATTTTGc                                                                                                              >  1:238571/1‑140 (MQ=255)
                          ttttttGAGTATGAATATTAAAGATTATTTTACAAGTATTAAACTTGTTAAAGCCATCAATTTATTACTTTTTACATATCATTTTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTTATAAAAATTTTACAAAta                                                                                                         >  2:410304/4‑139 (MQ=255)
                                     tGAATTTTAGAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAAt                                                                                              >  1:532859/1‑140 (MQ=255)
                                          tttAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACtt                                                                                         <  1:454232/140‑1 (MQ=255)
                                            tAATGATTATTTTACTAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGc                                                                                       <  1:293775/140‑1 (MQ=255)
                                            tAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGc                                                                                       <  1:402336/140‑1 (MQ=255)
                                             aaaGATTATTTTACAAGGATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGACTTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTACGCATAACtgtaa                                                                                      >  2:6795/1‑136 (MQ=255)
                                              aaGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCAt                                                                                     >  1:155388/1‑140 (MQ=255)
                                               aGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCAtt                                                                                    >  1:488816/1‑140 (MQ=255)
                                                gATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACTTTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCAttt                                                                                   >  1:440502/1‑140 (MQ=255)
                                                      tttACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTcc                                                                             >  1:591208/1‑140 (MQ=255)
                                                                ttAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTc                                                                   <  1:63985/140‑1 (MQ=255)
                                                                  aaaCTTGTTAACGCCATCAAATTATTACTTTCTACAAAACATTCAATTACAAATGTTTATGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTACGAATTACTTGCATTTTAGCCCTAAACAGTTCCg                                                                 >  1:442292/1‑140 (MQ=255)
                                                                  aaaCTTGTTAACGCAATCAATTTATTACTTGCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCg                                                                 <  2:382445/140‑1 (MQ=255)
                                                                      ttGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCa                                                             >  2:396905/1‑140 (MQ=255)
                                                                           aaCGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCACTTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCgg                                                        >  2:678276/1‑139 (MQ=255)
                                                                           aaCGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGt                                                        >  2:599156/1‑140 (MQ=255)
                                                                              gCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTc                                                     <  1:139954/140‑1 (MQ=255)
                                                                                 aTCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCaa                                                  >  1:565106/1‑140 (MQ=255)
                                                                                 aTCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCaa                                                  >  1:14578/1‑140 (MQ=255)
                                                                                 aTCAATTTATTACTTTATACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCTTAAACAGTTCCGTTCACTCGTTTCTaa                                                  >  2:657459/1‑140 (MQ=255)
                                                                                        tattaCTTTCTACAAAACATTCTATTACAACTGTTTCTGAAATGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACt                                           >  1:497269/1‑140 (MQ=255)
                                                                                             cTTTCTACAAAACATCCTATTACATCTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAAGTAATTTAAGAATGACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAacc                                      <  1:183326/140‑1 (MQ=255)
                                                                                                 ctaacaaaCAAGCTATTACAACTGTTTCGGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAAccacca                                  <  1:91597/135‑1 (MQ=255)
                                                                                                 ccaCAAAACATTCTATCACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAAccacca                                  <  1:554433/138‑1 (MQ=255)
                                                                                                  tACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACcaccac                                 >  1:536623/1‑140 (MQ=255)
                                                                                                      aaaCATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAAt                             >  2:386234/1‑140 (MQ=255)
                                                                                                         cATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATaca                          >  1:154476/1‑140 (MQ=255)
                                                                                                                 tACAGCTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAAGGACTTGCATTTTAGTCCTAACCAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCcaac                  <  2:183974/140‑1 (MQ=255)
                                                                                                                  aCAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCcaaca                 >  1:688851/1‑140 (MQ=255)
                                                                                                                         tttCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAGATAAc          >  1:689525/1‑140 (MQ=255)
                                                                                                                          ttCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACGCCCACAAATACACTTCCAACAAGATAACg         >  1:700087/1‑140 (MQ=255)
                                                                                                                          ttCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAGATAACg         <  2:154708/140‑1 (MQ=255)
                                                                                                                           tCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCAGTCGTTTCCAAGATTACTGAACAAACCAAAATACACTTTAAAAAAGATacagt        >  1:293366/1‑136 (MQ=255)
                                                                                                                            cTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAGATAACGTa       >  1:676191/1‑140 (MQ=255)
                                                                                                                            cTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAGATAACGTa       >  2:314155/1‑140 (MQ=255)
                                                                                                                             tGAATTGGACGGTTTTAACAGTCATACACATTTTGCAAATCAATTTAAGAATTACTTGCATTGTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATAAACTTCCAACAAGATAACGTag      >  2:434272/1‑139 (MQ=255)
                                                                                                                                 ttGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAGATAACGTATcaca  <  2:705327/140‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                       
TCATATTGTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGCCGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAGATAACGTATCACA  >  CP000730/2502008‑2502276

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑