Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,233,332 C→A 57.9% P413T (CCT→ACT)  USA300HOU_1157 → non‑specific serine/threonine protein kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,233,3320CA57.9% 2.1 / 29.2 26P413T (CCT→ACT) USA300HOU_1157non‑specific serine/threonine protein kinase
Reads supporting (aligned to +/- strand):  ref base C (3/8);  new base A (8/7);  total (11/15)
Fisher's exact test for biased strand distribution p-value = 2.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.65e-01

ATGGCAATGTTTGGTAATAAATACGAAGAGACACCTGATGTAATCGGGAAATCTGTAAAAGAAGCAGAGCAAATATTCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATCCTGAAAATGAAATTATTAAGACAACTCCTAATACTGGTGAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGC  >  CP000730/1233200‑1233468
                                                                                                                                    |                                                                                                                                        
atggcaatgTTTGGTAATAAATACGAAGAGACACCTGATGTAAGCGGGAAATCTGTAAAAGAAGCAGAGCAAATATTCAATAAAAACAACCTGAAATTGGGGAAAATTTCTAGAAGTTATAGTGATAAATATACTGAAAAt                                                                                                                                  <  2:311354/141‑1 (MQ=255)
   gcaatgTTTGGTAATAAATACGAAGAGACACCTGATGTAATCGGGAAATCTGTAAAAGAAGCAGAGCAAATATTCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATCCTGAAAATGaa                                                                                                                               >  1:58574/1‑141 (MQ=255)
           tGGTAATAAATACGAAGAGACACCTGATGTAATCGGGAAATCTGTAAAAGAAGCAGAGCAAATATTCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGTTAAATATACTGAAAATGAAATTATTaa                                                                                                                       <  2:73509/141‑1 (MQ=255)
             gTAATAAATACGAAGAGACACCTGATGTAATCGGGAAATCTGTAAAAGAAGCAGAGCAAATATTCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATCCTGAAAATGAAATTATTAAGa                                                                                                                     <  1:278112/141‑1 (MQ=255)
              taataaATACGAAGAGACACCTGATGTAATCGGGAAATCTGTAAAAGAAGCAGAGCAAATATTCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATCCTGAAAATGAAATTATTAAGAc                                                                                                                    >  1:11711/1‑141 (MQ=255)
                  aaataCGAAGAGACACCTGATGTAATCGGGAAATCTGTAAAAGAAGCAGAGCAAATATTCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATACTGAAAATGAAATTATTAAGACAACt                                                                                                                >  1:145573/1‑141 (MQ=255)
                         aaGACAAACCTGATGTAATCGGGAAATCTGTAAAAGAAGAAGAGCAAATATTCAATAAAAACAACCTGAAATCGGGTAAAATTTCTAGAAGTTATAGTGATAAATATCCTGAAAATGAAATTATTAAGACAACTCCTAATa                                                                                                         <  2:281964/141‑1 (MQ=255)
                             gaCACCTGATGTAATCGGGAAATCTGTAAAAGAAGCAGAGCAAATATTCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATACTGAAAATGAAATTATTAAGACAACTCCTAATAATgg                                                                                                     <  1:248515/141‑1 (MQ=255)
                               cacCTGATGTAATCGGGAAATCTGTAAAAGAAGCAGAGCAAATATTCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATACTGAAAATGAAATTATTAAGACAACTCCTAATACTGGTg                                                                                                   >  1:152346/1‑141 (MQ=255)
                                         aaTCGGGAAATCTGTAAAAGAAGCAGAGCAAATATTCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATACTGAAAATGAAATTATTCAGACAACTCCTAATACTGGTGAACGTGTTGa                                                                                         >  2:54878/1‑141 (MQ=255)
                                           tCGGGAAATCTGTAAAAGAAGCAGAGCAAATATTCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATACTGAAAATGAAATTATTAAGACAACTCCTAATACTGGTGAACGTGTTGAAc                                                                                       >  2:143802/1‑141 (MQ=255)
                                               gAAATCTGTAAAAGAAGCAGAGCAAATATTCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATCCTGAAAATGAAATTATTAAGACAACTCCTAATACTGGTGAACGTGTTGAACgtgg                                                                                   <  1:168704/141‑1 (MQ=255)
                                                  aTCTGTAAAAGAAGCAGAGCAAATATTCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATCCTGAAAATGAAATTATTAAGACAACTCCTAATACTGGTGAACGTGTTGAACGTGGTGa                                                                                <  2:11711/141‑1 (MQ=255)
                                                   tCTGTAAAAGAAGCAGAGCAAATATTCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATACTGAAAATGAAATTATTAAGACAACTCCTAATACTGGTGAACGTGTTGAACGTGATGAc                                                                               >  2:65431/1‑141 (MQ=255)
                                                       tAAAAGAAGCAGAGCAAATATTCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATCCTGAAAATGAAATTATTAAGACAACTCCTAATACTGGTGAACGTGTTGAACGTGGTGACAgtg                                                                           >  1:336709/1‑141 (MQ=255)
                                                         aaaGAAGCAGAGCAAATATTCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATACTGAAAATGAAATTATTAAGACAACTCCTAATACTGGTGAACGTGTTGAACGTGGTGACAGTGtt                                                                         <  1:185404/141‑1 (MQ=255)
                                                            aaagCAGAGCAAATATTCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATCCTGAAAATGAAATTATTAAGACAACTCCTAATACTGGTGAACGTGTTGAACGTGGTGACAGTGTTGAt                                                                      <  2:99328/140‑1 (MQ=255)
                                                                 agagCAAATATTCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAAGATACTGAAAATGAAATTATTAAGACAACTCATAATACTGGTGAACGTGTTGAACGTGTTAGAACTGTTGAtgttgt                                                                 >  2:201970/1‑141 (MQ=255)
                                                                    acaacaatacAATAAAAACAACCTGAGATTGGGTAAAATTTCTAGAACTAAAAGTGATAAATATCCGGAAAATGAAATTATTAATACAACTCCTAATACTGGTGAACCTGTTGAACGTGGTGACAGTGTTGATGTTGTtat                                                              <  2:24439/132‑1 (MQ=255)
                                                                           ttCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATACTGAAAATGAAATTATTAAGACAACTCCTAATACTGGTGAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAg                                                       <  1:247003/141‑1 (MQ=255)
                                                                               aTAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATACTGAAAATGAAATTATTAAGACAACTCCTAATACTGGTGAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGcc                                                   <  1:318251/141‑1 (MQ=255)
                                                                                               aTTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATACTGAAAATGAAATTATTAAGACAACTCCTAATACTGGTGAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAAt                                   <  2:189828/141‑1 (MQ=255)
                                                                                                    gTAAAATTTCTAGAAGTTATAGTGATAAATATCCTGAAAATGAAATTATTAAGACAACTCCTAATACTGGTGAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCaa                              <  2:58574/141‑1 (MQ=255)
                                                                                                        aaTTTCTAGAAGTTATAGTGATAAATATCCTGAAAATGAAATTATTAAGACAACTCCTAATACTGGTGAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGt                          <  2:322802/141‑1 (MQ=255)
                                                                                                                    ttATAGTGATAAATATACTGAAAATGAAATTATTAAGACAACTCCTAATACTGGTGAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTAcc              >  2:129319/1‑141 (MQ=255)
                                                                                                                                atatACTGAAAATGAAATTATTAAGACAACTCCTAATACTGGTGAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGc  >  1:260205/1‑141 (MQ=255)
                                                                                                                                    |                                                                                                                                        
ATGGCAATGTTTGGTAATAAATACGAAGAGACACCTGATGTAATCGGGAAATCTGTAAAAGAAGCAGAGCAAATATTCAATAAAAACAACCTGAAATTGGGTAAAATTTCTAGAAGTTATAGTGATAAATATCCTGAAAATGAAATTATTAAGACAACTCCTAATACTGGTGAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGC  >  CP000730/1233200‑1233468

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: