Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,274,212 A→T 58.8% K205N (AAA→AAT)  codY → GTP‑sensing transcriptional pleiotropic repressor CodY

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,274,2120AT58.8% 16.3 / 30.0 29K205N (AAA→AAT) codYGTP‑sensing transcriptional pleiotropic repressor CodY
Reads supporting (aligned to +/- strand):  ref base A (3/9);  new base T (10/7);  total (13/16)
Fisher's exact test for biased strand distribution p-value = 1.30e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTCTTAG  >  USA300TCH1516_ALE/1274081‑1274348
                                                                                                                                   |                                                                                                                                        
cgaGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTCATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTATTCGCATCAAATGTTGCAGAt                                                                                                                                 <  1:196946/139‑1 (MQ=255)
      aaaGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGTAAGGCCTATTAATCGCATTAACAGTTGCAGATAGAGtt                                                                                                                           <  1:156509/141‑1 (MQ=255)
          aagCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTa                                                                                                                       <  2:77961/141‑1 (MQ=255)
                         ttgcaATTCCAATGGCAATTAATTGAGTATCTTATTGTGAAAAAGAACCGATGGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTaa                                                                                                        <  2:23828/140‑1 (MQ=255)
                         ctgctATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTaa                                                                                                        <  1:120915/141‑1 (MQ=255)
                               ttAAAAAGGCAATTAATTCATTATCTTATTCTGACAAAGAAGTGATTGAACACATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTaa                                                                                                  <  1:189865/141‑1 (MQ=255)
                                 aCAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAAt                                                                                                >  1:213155/1‑141 (MQ=255)
                                 aCAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAAt                                                                                                <  1:264108/141‑1 (MQ=255)
                                     tGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCAc                                                                                            <  1:98176/141‑1 (MQ=255)
                                     tGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCAc                                                                                            <  1:98205/141‑1 (MQ=255)
                                      ggCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACt                                                                                           >  2:272307/1‑141 (MQ=255)
                                              attCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAAt                                                                                   >  2:260145/1‑141 (MQ=255)
                                                   ttttCTTAGTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGaa                                                                              <  2:121487/138‑1 (MQ=255)
                                                     aTCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAg                                                                            >  2:257773/1‑141 (MQ=255)
                                                             cTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGgtg                                                                    <  2:37923/141‑1 (MQ=255)
                                                                 aaaaGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAAt                                                                >  2:14038/1‑141 (MQ=255)
                                                                    agaagCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGa                                                             >  1:231866/1‑141 (MQ=255)
                                                                       agCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATc                                                          >  1:61225/1‑141 (MQ=255)
                                                                                  atatCTTTGAAGCACTTGGCGGTACGGAAGGCCGATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAg                                               <  2:157193/141‑1 (MQ=255)
                                                                                                cTTGGCGGTAAGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACt                                 <  1:252084/141‑1 (MQ=255)
                                                                                                   ggCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTc                              >  1:83811/1‑141 (MQ=255)
                                                                                                     cGGTCCGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGGATCACGTTCTTTAGGAATGAAAGGTACTTTCAt                            >  1:190730/1‑141 (MQ=255)
                                                                                                         aCGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTaaa                        <  2:181284/141‑1 (MQ=255)
                                                                                                          cGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTTGTATTACTAGATCTGTAATTGTAAATGCACTACGTAGATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAGTGAAAGGTACTTTCGTTAAAg                       >  1:212700/1‑141 (MQ=255)
                                                                                                          cGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAGTTGTAAATGCACTACGTAAATTAGAAAGGGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTaaaa                       >  1:107871/1‑140 (MQ=255)
                                                                                                          cGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAg                       >  1:212709/1‑141 (MQ=255)
                                                                                                                       aaTCGCATCAAATGTTGCAGAAAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCTCGTTGTTTTGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGaaaa          >  1:145621/1‑141 (MQ=255)
                                                                                                                          cGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAAtt       <  1:187663/141‑1 (MQ=255)
                                                                                                                               cAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTCTTAg  <  1:144656/141‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                        
GTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTCTTAG  >  USA300TCH1516_ALE/1274081‑1274348

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: ‑