Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,274,207 T→A 100% S204T (TCA→ACA)  USA300HOU_1186 → CodY family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,274,2070TA100.0% 54.7 / NA 19S204T (TCA→ACA) USA300HOU_1186CodY family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (10/9);  total (10/9)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCATAGTGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATT  >  CP000730/1274071‑1274343
                                                                                                                                        |                                                                                                                                        
gCATAGTGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACaaa                                                                                                                                      >  2:162098/1‑141 (MQ=255)
  aTAGTGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAg                                                                                                                                    >  2:319445/1‑141 (MQ=255)
   tAGTGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGt                                                                                                                                   >  1:9933/1‑141 (MQ=255)
        aaGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAg                                                                                                                              <  2:301785/141‑1 (MQ=255)
                                     gctATTACAATGGCAATTAATTCATTATCCTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAAtt                                                                                                 <  1:162098/141‑1 (MQ=255)
                                             aaTGGCAATTAATTCATTATCTTATTCTGAGAAAGAAGCGATTGAACATATCTTAGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCGACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGc                                                                                         <  2:245907/141‑1 (MQ=255)
                                                  cAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTAc                                                                                    >  1:124087/1‑141 (MQ=255)
                                                             ttATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAGTTGTAAATGCACTACGTGCATTAgga                                                                         >  1:96294/1‑139 (MQ=255)
                                                                          aaaaaGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTAATAATCGCAACAAAAGTTGCAGACAGCCACGCCACCGCTAGATCGTTAAGTGGAAATGCACTACGTAAATTAGAAAGTGCTgggctaa                                                            >  2:234974/1‑136 (MQ=255)
                                                                            aaaGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAAtt                                                          >  2:96941/1‑141 (MQ=255)
                                                                                 agCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCCGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCCCTACGTACCTCTGAATGTTTTGGTGTAGTTGAATc                                                     >  2:318625/1‑141 (MQ=255)
                                                                                 agCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATc                                                     <  2:108344/141‑1 (MQ=255)
                                                                                  gCGATTACACATATCTTTGAAGAACTTGGGTGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATAACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCa                                                    <  2:35204/141‑1 (MQ=255)
                                                                                   cGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCAc                                                   <  1:266166/141‑1 (MQ=255)
                                                                                              atCTTTGAAGAACTTAGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTCCGTAAATTAGAAAGTGCTGGTGTACTTGCATCACGTTCTTTAGGa                                        >  1:247075/1‑141 (MQ=255)
                                                                                                   tGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGaa                                   <  2:205134/141‑1 (MQ=255)
                                                                                                          cTTGGAGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAgtacct                            <  1:69966/141‑6 (MQ=255)
                                                                                                                              aTTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTTCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGa        <  2:36848/141‑1 (MQ=255)
                                                                                                                                    cGCAACACAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAGTTGAATCACGTTCTTTAGGAATGAAAGGTACTTTGATTAAAGTTAAAAAAGAAAAAtt  >  1:210457/1‑141 (MQ=255)
                                                                                                                                        |                                                                                                                                        
GCATAGTGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATT  >  CP000730/1274071‑1274343

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: