Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,229,054 A→G 8.4% N37S (AAT→AGT)  rsmB → Ribosomal RNA small subunit methyltransferase B

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,229,0540AG 8.4% 125.3 / 2.9 49N37S (AAT→AGT) rsmBRibosomal RNA small subunit methyltransferase B
Reads supporting (aligned to +/- strand):  ref base A (25/19);  new base G (2/2);  total (27/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.85e-01

CACACTAGTAGGGAAGAAACTTATATGATAGAAAACGTGAGAAGTCTTGCTTTTGACACGATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTTGTGAAAACAAAGATTAAGGCATGGGTTAGGCAATTATTATGGATGAGTAT  >  USA300TCH1516_ALE/1228921‑1229189
                                                                                                                                     |                                                                                                                                       
cagacgagtagGGAAGAAACTTATATGATAGAAAACGTGAGAAGTCTGGCTTTTGACACGATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATTAAGTGTTGTCAGAAAAGGAATTAAATGCAAt                                                                                                                                   <  2:500823/134‑1 (MQ=255)
cacgcTAGTAGGGAAGAAACTTATATGAGAGAAAACGTGAGAAGTCTTGCTTTTGACACGATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAAt                                                                                                                                   <  2:453572/140‑1 (MQ=255)
  cacTAGTAGGGAAGAAACTTATATGATAGAAAACGTGAGAAGTCTTGCTTTTGACACGATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATgg                                                                                                                                 <  1:488674/140‑1 (MQ=255)
  cacTAGTAGGGAAGAAACTTATATGATAGAAAACGTGAGAAGTCTTGCTTTTGACACGATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATgg                                                                                                                                 <  1:472016/140‑1 (MQ=255)
     tagtagGGAAGAAACTTATATCACTCAACAGGATTTTAGGGTTGCTTTGGAAACGATTCAAGATATAGGTAAGGAATGGACGGATAGTTACTTGCGTACCAATGAAGTGATGTCAGAAAAGCGATTGTAGGCAATGGATa                                                                                                                              >  2:498274/1‑140 (MQ=255)
              agaaACTTATATGATAGAAAACGTGAGAAGTCTTGCTTTTGACACGATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATACGGCtttat                                                                                                                     >  1:192937/1‑140 (MQ=255)
                aaaCTGATATGATAGAAAACGTGAGAAGTCTTGCTTTTGACACGATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCtttattt                                                                                                                   <  1:108269/140‑1 (MQ=255)
                     tataTGATAGAAAACGTGAGAAGTCTTGCTTTTGACACGATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGa                                                                                                              >  1:129938/1‑140 (MQ=255)
                            tAGAAAACGGGAGGAGTCTTGCTTGTGACGCGATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAGTGCAATGGATAAGGCTTTATTTACAGAAATTGTc                                                                                                       <  2:131823/140‑1 (MQ=255)
                             aGAAAACGTGAGAAGTCTTGCTTTTGACACGATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGATTTACTTACAGAAATTGTCt                                                                                                      >  2:509049/1‑140 (MQ=255)
                                  aCGTGAGAAGTCTTGCTTTTTACACTATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGa                                                                                                 <  1:210732/140‑1 (MQ=255)
                                  aCGTGAGAAGTCTTGCTTTTGACACGATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGa                                                                                                 >  1:337830/1‑140 (MQ=255)
                                  aCGTGAGAAGTCTTGCTTTTGACACGATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGa                                                                                                 <  1:542109/140‑1 (MQ=255)
                                      gagaAGTCTTGCTTTTGACACGATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCTTTGAAGCGTCCTCAGAAAATGAATTAAGTGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCg                                                                                             >  1:131823/1‑140 (MQ=255)
                                      gagaAGTCTTGCTTTTGACACGATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAGTGCAATGGATAAGGCTTTATTTACAGAAATTGTc                                                                                                       >  1:418509/1‑130 (MQ=255)
                                      gagaAGTCTTGCTTTTGACACGATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAGTGCAATGGATAAGGCTTTATTTACAGAAATTGTc                                                                                                       <  2:418509/130‑1 (MQ=255)
                                       agaAGGCTTGCTTGTGAAAAGATTCAAGATATATTAAAGGAAGATGACTATAAAAAATTGCGTGTCAATGAAGTGTTGTAAGAAAATGAATTAAATGCAATGGATAAGGATTTATTTACAGAAATTGTCTACGGAACCGt                                                                                            <  2:492627/140‑1 (MQ=255)
                                        gaAGTCTTGATTTTGACACGATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGtt                                                                                           <  1:72338/140‑1 (MQ=255)
                                                   gttaacacGGTTCTAAATATATTAAATGAAGAGGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAata                                                                                <  2:519691/136‑1 (MQ=255)
                                                           gATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACAGAACCGTTAAAAGCAAAAATACGTTAg                                                                        >  2:274259/1‑140 (MQ=255)
                                                                    gatcttAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGGTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAACTTGTCTACGGAACCGTTCAAAGAAAATATACGTTAGATTtttatt                                                               >  1:369305/5‑140 (MQ=255)
                                                                     atatTAAATGAAGTGTCGTATATTAACTTGGGTAGCAATGAAGGGTGGTCATAAAATGAATTAAATGCAATTGATAAGGCTTTCTTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTtttattt                                                              <  2:527803/140‑1 (MQ=255)
                                                                     atatTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTAAGATGtttattt                                                              >  2:386776/1‑140 (MQ=255)
                                                                      tatTAAGTGAAGGTTCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATGAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTtttattta                                                             <  2:538198/140‑1 (MQ=255)
                                                                         tAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTTTTTAAAg                                                          >  2:159348/1‑140 (MQ=255)
                                                                           aaTGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGcc                                                        <  2:506748/140‑1 (MQ=255)
                                                                                aGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAGAATATACGTTAGATTTTTATTTAAAGCCTTTtg                                                   >  1:537375/1‑140 (MQ=255)
                                                                                 ggTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTtgt                                                  <  2:20119/140‑1 (MQ=255)
                                                                                 ggTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTtgt                                                  >  2:194544/1‑140 (MQ=255)
                                                                                 ggTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAAACGTTAAAAGAAAATATAAGTTAGATTTTTATTTAAAGTATTTtgt                                                  >  2:294152/1‑140 (MQ=255)
                                                                                 ggTGCGTATAGTAACTTGCGTATCAATGAAGTGTGGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTtgt                                                  >  2:378910/1‑140 (MQ=255)
                                                                                   tGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTTGTGa                                                >  2:156230/1‑140 (MQ=255)
                                                                                     cGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAACGCCTTTTGTGaaa                                              >  2:464667/1‑140 (MQ=255)
                                                                                       tataGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACTTGAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTTGTGAAAAc                                            <  1:568430/140‑1 (MQ=255)
                                                                                       tataGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTTGTGAAAAc                                            >  2:154073/1‑140 (MQ=255)
                                                                                          aGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTTGTGAAAACaaa                                         >  1:462191/1‑140 (MQ=255)
                                                                                              attttagTATCAATCATGTATTGTCAGAAAATGAATTAAAGGCAATGGATAAGGCTCGATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTTGTGAAAACAAAGAtt                                     <  1:40769/134‑1 (MQ=255)
                                                                                                   cGTATCCATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTTGTGAAAACAAAGATTAAGGc                                >  2:481933/1‑140 (MQ=255)
                                                                                                   cGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTTGTGACAACAAAGATTAAGGc                                >  2:549945/1‑140 (MQ=255)
                                                                                                     tATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTTGTGAAAACAAACATTAAGGCag                              >  2:441668/1‑139 (MQ=255)
                                                                                                     tATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTACTTAAATCCTTTTGTGAAAACAAAGATTAAGGCAt                              >  2:116310/1‑140 (MQ=255)
                                                                                                        aaagtaaGTGTTGTGAGAAAATGAATTAACTGCAACGGATAAGGCTTTATTTACAGAAAGTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTTGTGAAAACAAAGATTAAGGCATggg                           <  2:264720/135‑1 (MQ=255)
                                                                                                         aaTGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTTGTGAAAACAAAGATTAAGGCATGGGt                          >  2:13406/1‑140 (MQ=255)
                                                                                                            tgaGTGTTGTCAGAAGATGAAGTAAATGCAATGGATAAGGCTTTAATTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTTGTGAAAACAAAGATTAAGGCATGGGTTAg                       <  2:59040/138‑1 (MQ=255)
                                                                                                                     tCAGAAAATGAATGAAATGAAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTTGTGAAAACAAAGATTAAGGCATGGGTTAGGCAattatt              <  1:236109/140‑1 (MQ=255)
                                                                                                                      cAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTTGTGAAAACAAAGATTAAGGCATGGGTTAGGCAAttatta             <  2:462191/140‑1 (MQ=255)
                                                                                                                      cAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTTGTGAAAACAAAGATTAAGGCATGGGTTAGGCAAttatta             >  1:54293/1‑140 (MQ=255)
                                                                                                                                aTTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTTGTGAAAACAAAGATTAAGGCATGGGTTAGGCAATTATTATGGATGAGTa   >  2:569754/1‑140 (MQ=255)
                                                                                                                                 atAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGTAAATACCCGTTAGATTTTTATTTAAAGCCTTTTGTGAAAACAAAGATTAAGGCATGGGTTAGGCAATTATTATGGATGAGTAt  >  1:446996/2‑140 (MQ=255)
                                                                                                                                     |                                                                                                                                       
CACACTAGTAGGGAAGAAACTTATATGATAGAAAACGTGAGAAGTCTTGCTTTTGACACGATTCAAGATATATTAAATGAAGGTGCGTATAGTAACTTGCGTATCAATGAAGTGTTGTCAGAAAATGAATTAAATGCAATGGATAAGGCTTTATTTACAGAAATTGTCTACGGAACCGTTAAAAGAAAATATACGTTAGATTTTTATTTAAAGCCTTTTGTGAAAACAAAGATTAAGGCATGGGTTAGGCAATTATTATGGATGAGTAT  >  USA300TCH1516_ALE/1228921‑1229189

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑