Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 479,553 G→A 100% A194T (GCA→ACA)  USA300HOU_0458 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730479,5530GA100.0% 100.0 / ‑6.5 34A194T (GCA→ACA) USA300HOU_0458hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (17/16);  minor base T (0/1);  total (17/17)
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.

GCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATGCATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGACTACC  >  CP000730/479421‑479688
                                                                                                                                    |                                                                                                                                       
gCAATAATAGATGAACAAGGTGAGCCACTTAGCGACCAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGCTAAATTTCTATCGAGTTGGACAATGGCGCCGTGCGACCAAAGGTTTTACCATACATGGTTg                                                                                                                                 >  2:314247/1‑141 (MQ=255)
gCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTg                                                                                                                                 <  2:122183/141‑1 (MQ=255)
          aTGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAgcgc                                                                                                                       <  2:16942/141‑1 (MQ=255)
          aTGAACAAGGTGAGCCACTTAGCGAACAAGTGAAGCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAgcgc                                                                                                                       >  1:267937/1‑141 (MQ=255)
            gAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGACGAAGCGTGAGCAAAGTTTTTACAATACAGGGGTGCATTTAGCGCaa                                                                                                                     >  2:47201/1‑141 (MQ=255)
                 aGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGa                                                                                                                >  1:268964/1‑141 (MQ=255)
                  ggTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATgct                                                                                                               >  2:346072/1‑139 (MQ=255)
                    ggAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAATCTTGATATCGATCAATTTCTATCGAGTTGTAGAATGCCGAAGCGTGATCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCa                                                                                                             <  2:56127/140‑1 (MQ=255)
                        ccACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGt                                                                                                         <  1:274683/141‑1 (MQ=255)
                           cTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGtttt                                                                                                      <  1:247384/141‑1 (MQ=255)
                                   aCAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGc                                                                                              >  2:89641/1‑141 (MQ=255)
                                     aaGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGcac                                                                                            >  2:149822/1‑141 (MQ=255)
                                        ggAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAgc                                                                                         <  1:280909/140‑1 (MQ=255)
                                              gTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAg                                                                                   <  2:267937/141‑1 (MQ=255)
                                                        tAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAgg                                                                         >  1:193991/1‑141 (MQ=255)
                                                           aTGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCtt                                                                      >  1:6099/1‑141 (MQ=255)
                                                                    aCTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGa                                                             >  1:43913/1‑141 (MQ=255)
                                                                    aCTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGa                                                             >  1:216794/1‑141 (MQ=255)
                                                                    aCTTTATATCGAACAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGAAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAACGGATTACCCAAAGa                                                             >  2:133146/1‑141 (MQ=255)
                                                                       ttATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATcc                                                          <  2:319532/141‑1 (MQ=255)
                                                                            tCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGaaa                                                     >  1:316935/1‑141 (MQ=255)
                                                                                 cAATTTCTAGCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACg                                                <  2:129324/141‑1 (MQ=255)
                                                                                  aaTTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGa                                               <  2:144561/141‑1 (MQ=255)
                                                                                        tATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGt                                         >  1:298491/1‑141 (MQ=255)
                                                                                                  gagaaTGTCGAAGAGTGAACTAAGTTTTTCCCGTTCATGGTTTCATGTAGCGAAATATCCACATACTTTTACTATAGCACTGCGCCAAGTGATTACACGCTGACGCAATGATTCTGAAATGACGATAGAGTCAGTATTCAc                               <  2:78477/138‑1 (MQ=255)
                                                                                                  gACAATGCCGAAGCGTGAGCAAAGTTTTTCCCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGTGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAAc                               <  1:207276/141‑1 (MQ=255)
                                                                                                          cGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCAAGGAGCATAGAGGCTCACCCAATGATAATGAGATGACGATAGAGTCAGTATTAACTCAgtttt                       <  2:72445/141‑1 (MQ=255)
                                                                                                           gAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAGATGAGGATAGAGTCAGTATTCACTCAGGTTTc                      >  1:161305/1‑141 (MQ=255)
                                                                                                               cctGAGCAAAGTTCTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATa                  <  2:187247/139‑1 (MQ=255)
                                                                                                               cGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATa                  <  2:316935/141‑1 (MQ=255)
                                                                                                                  gatcAAAGTTTTTACCATACCTTGTTGCATTTAGCGCAACATCACCCTCGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACTCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGAt               <  2:16872/138‑1 (MQ=255)
                                                                                                                     cAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGTAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAg            <  2:6099/141‑1 (MQ=255)
                                                                                                                           ttttACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGAc      >  1:328932/1‑141 (MQ=255)
                                                                                                                               aCCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAAACTCAGTATCACCCCATTTTACGATAGATCAGGAAGACTAcc  >  1:45574/1‑141 (MQ=255)
                                                                                                                                    |                                                                                                                                       
GCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATGCATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGACTACC  >  CP000730/479421‑479688

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: