Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 622,019 T→C 9.7% L861S (TTG→TCG)  sdrE → Serine‑aspartate repeat‑containing protein E

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE622,0190TC 9.7% 113.2 / 2.9 41L861S (TTG→TCG) sdrESerine‑aspartate repeat‑containing protein E
Reads supporting (aligned to +/- strand):  ref base T (22/15);  new base C (2/2);  total (24/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01

GCAGATAATATGACATTAGACAGTGGTTTCTATAAAACACCAAAATACAGTTTAGGTGATTATGTTTGGTACGACAGTAATAAAGACGGCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGTTATTTTTGAAAAGCCTGCTGGCTTAACACAAACAGTTACAAATACA  >  USA300TCH1516_ALE/621883‑622158
                                                                                                                                        |                                                                                                                                           
gCAGATAATATGACATTAGACAGTGGTTTCTATAAAACACAAAAATACAGTTTAGGTGATTATGTTTGGTACGACAGTAATAAAGACGGCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCaa                                                                                                                                         <  1:371284/141‑1 (MQ=255)
gCAGATAATATGACATTAGACAGTGATTTCTATAAAACACCAAAATACAGTTTAGGTGATTATGTTTGGTACGACAGTAATAAAGACGGCAAACAAAATAAAAAAGAAAAAGGTATCAAAGATGTGACAGTTACATTGCaa                                                                                                                                         <  2:406478/141‑1 (MQ=14)
   gATAATATGACATTAGACAGTGGTTTCTATAAAACACCAAAATACAGTTTAGGTGATTATGTTTGGTACGACAGTAATAAAGACGGCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAAc                                                                                                                                      >  2:28727/1‑141 (MQ=255)
   gATAATATGACATTAGACAGTGGTTTCTATAAAACACCAAAATACAGTTTAGGTGATTATGTTTGGTACGACAGTAATAAAGACGGCAAACAAGATTCAACTG‑AAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACg                                                                                                                                     >  2:151234/1‑141 (MQ=255)
        tttGACATTAGACAGTGGTTTCAAAAAAACACCAAAATACATTTTAGGAGATTATGTTTTGTACGACAGTAATAAAGATGGCAAACAAGATTCAACTG‑AAAAGGTATCAAAGATGTGACAGTTACATTAAAAAACGaaaaa                                                                                                                                <  2:368919/139‑1 (MQ=14)
         aagACATAAGACAGTGGTTTCTATAAAACACCAAAAAACAGTAAAGGTGATTATGTTTGATACGACAGTAATAAAGACGGCAAACAAAATTCAACAGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGaaaaa                                                                                                                                <  2:422030/139‑1 (MQ=17)
           gtcATTAGACAGTGGTTTCTATAAAACACCAAAATACAGTTTAGGTGATTATGTTTGGTACGACAGTAATAAAGACGGCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAgg                                                                                                                              <  2:189136/139‑1 (MQ=255)
                tAGACAGTGGTTTCTATAAAACACCAAAATACAGTTTAGGTGATTGTGTTTGGTACGACAGTAATAAAGACGGCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATCGCAAAACGAAAAAGGCGAAg                                                                                                                         >  2:330275/1‑141 (MQ=255)
                tAGACAGTGGTTTCTATAAAACACCAAAATACAGTTTAGGTGATTATGTTTGGTACGACAGTAATAAAGACGGCAAACAAGATTCAACTGAAAAAGGTATAAAAGATGTGACAGTTACATCGCAAAACGAAAAAGGCGAAg                                                                                                                         >  2:370453/1‑141 (MQ=255)
                    cAGTGGTTTCTATAAAACACCAAAATACAGTTTAGGTGATTATGTTTGGTACGACAGTAATAAAGACGGCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAAt                                                                                                                     >  1:459797/1‑141 (MQ=255)
                      gTGGTTTCTATAAAACACCAAAATACAGTTTAGGTGATTATGTTTGGTACGACAGTAATAAAGACGGCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTg                                                                                                                   <  2:293687/141‑1 (MQ=255)
                      gTGGTTTCTATAAAACACCAAAATACAGTTTAGGTGATTATGTTTGGTACGACAGTAATAAAGACGGCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTg                                                                                                                   <  1:82637/141‑1 (MQ=255)
                               ataAAACACCAAAATACAGTTTAGGTGATTATGTTTGGTACGACAGTAATAAAGACGGCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTa                                                                                                          >  2:178681/1‑141 (MQ=255)
                                           aaTACAGTTTAGGTGATTATGTTTGGTACGACAGTAATAAAGACGGCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGaaa                                                                                              >  2:432356/1‑141 (MQ=255)
                                                         gATTATGTTTGGTACGACAGTAATAAAGACGGCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGt                                                                                >  2:118828/1‑141 (MQ=255)
                                                         gATTATGTTTGGTACGACAGTAATAAAGACGGCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAAAAGTTTAAAATGGTAAATATCGt                                                                                >  1:350700/1‑141 (MQ=255)
                                                         gATAATGTTTGGTACGACAGTAATAAAGACGGCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGt                                                                                >  2:422848/1‑141 (MQ=255)
                                                          aTTATGTTTGGTACGACAGTAATAAAGACGGCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGtt                                                                               <  1:141563/141‑1 (MQ=255)
                                                                        gACAGTAATAAAGACGGCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGAt                                                                 >  2:301699/1‑141 (MQ=255)
                                                                             taataaAGACGGCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCgg                                                            <  1:442595/141‑1 (MQ=255)
                                                                                        gCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAg                                                 >  1:260002/1‑141 (MQ=255)
                                                                                         cAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACGTTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGt                                                >  2:132324/1‑141 (MQ=255)
                                                                                         cAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGt                                                >  2:316299/1‑141 (MQ=255)
                                                                                         cAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGt                                                >  2:61623/1‑141 (MQ=255)
                                                                                         cAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGt                                                >  1:83021/1‑141 (MQ=255)
                                                                                         cAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGt                                                >  1:423886/1‑141 (MQ=255)
                                                                                           aaCAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGTTa                                              >  1:19643/1‑141 (MQ=255)
                                                                                            aCAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATCGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGTTAt                                             <  1:370453/141‑1 (MQ=255)
                                                                                            aCAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATCGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAAGACAAAGTTAt                                             <  1:330275/141‑1 (MQ=255)
                                                                                                      aCTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGTTATTTTTGAAAAg                                   <  1:178681/141‑1 (MQ=255)
                                                                                                                gTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGTTATTTTTGAAAAGCCTGCTGGCt                         >  1:393326/1‑141 (MQ=255)
                                                                                                                 tATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGACCATGGTAAATATCCTTTAGATGCTTTCGCTCGCGGTAACTACGCAGTTCTTTATGATCGGCGTGGTGGCtt                        >  1:137114/1‑141 (MQ=12)
                                                                                                                 tATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGTTATTTTTGAAAAGCCTGCTGGCtt                        >  1:215535/1‑141 (MQ=255)
                                                                                                                        gATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGTTATTTTTGAAAAGCCTGCTGGCTTAACACaa                 <  1:430114/141‑1 (MQ=255)
                                                                                                                        gATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGTTATTTTTGAAAAGCCTGCTGGCTTAACACaa                 <  1:290513/141‑1 (MQ=255)
                                                                                                                        gATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGTTATTTTTGAAAAGCCTGCTGGCTTAACACaa                 <  1:192592/141‑1 (MQ=255)
                                                                                                                        gATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGTTATTTTTGAAAAGCCTGCTGGCTTAACACaa                 >  2:47342/1‑141 (MQ=255)
                                                                                                                            ggACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGTTATTTTTGAAAAGCCTGCTGGCTTAACACAAACAg             <  2:269993/140‑1 (MQ=255)
                                                                                                                             gACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGTTATTTTTGAAAAGCCTGCTGGCTTAACACAAACAGt            >  1:460611/1‑141 (MQ=255)
                                                                                                                              aCAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGTTATTTTTGAAAAGCCTGCTGGCTTAACACAAACAGtt           >  2:124838/1‑141 (MQ=255)
                                                                                                                                 gTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGTTATTTTTGAAAAGCCTGCTGGCTTAACACAAACAGTTACa        <  2:459797/141‑1 (MQ=255)
                                                                                                                                       ttGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGTTATTTTTGAAAAGCCTGCTGGCTTAACACAAACAGTTACAAATACa  <  1:422848/141‑1 (MQ=255)
                                                                                                                                       ttGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGTTATTTTTGAAAAGCCTGCTGGCTTAACACAAACAGTTACAAATACa  <  1:118828/141‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                           
GCAGATAATATGACATTAGACAGTGGTTTCTATAAAACACCAAAATACAGTTTAGGTGATTATGTTTGGTACGACAGTAATAAAGACGGCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTGACAGTTACATTGCAAAACGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAATGGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGTTATTTTTGAAAAGCCTGCTGGCTTAACACAAACAGTTACAAATACA  >  USA300TCH1516_ALE/621883‑622158

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