Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 622,464 G→A 22.7% S1009S (TCG→TCA)  sdrE → Serine‑aspartate repeat‑containing protein E

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE622,4640GA22.7% 83.2 / 4.1 48S1009S (TCG→TCA) sdrESerine‑aspartate repeat‑containing protein E
Reads supporting (aligned to +/- strand):  ref base G (17/18);  new base A (8/4);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 3.31e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.92e-01

GACAGTGATTCAGATTCAGACAGCGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGA  >  USA300TCH1516_ALE/622327‑622598
                                                                                                                                         |                                                                                                                                      
gaaagTGATGCAGATTCAGACAGCGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGAc                                                                                                                                     <  2:213395/138‑1 (MQ=255)
    gtcattcagactcagACAGCGACTCATATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAg                                                                                                                                 <  1:257223/138‑1 (MQ=255)
    gTGATTCAGATTCAGACAGCGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAg                                                                                                                                 <  1:303774/141‑1 (MQ=255)
     tGATTCAGATTCAGACAGCGACTCAGATTCAGAGAGCGACTCAGATTCGGACAGCGATTCATACACAGATAGCGACCCAGACGCAGACAGCAACACAGACTAAGACAGCGACTCAGATTCAAATAGGGATTCAGACTCaca                                                                                                                                >  2:159453/1‑139 (MQ=11)
         gaaacatcagaCAGCGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGCTTCAGACTCAGATAGCGACTCAGACTCAGATAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGACTCAAACAcagccagc                                                                                                                            >  2:5616/7‑141 (MQ=14)
            gattcagaCAGGGACTCAGATTCAGATAGCGGCTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAGCGAt                                                                                                                         <  1:396317/141‑1 (MQ=255)
              ttcagaCAGCGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCCGACTCAGACAGCGACTCagattcagatagcgattcagattcagatagcgattc                                                                                                                       >  2:205941/1‑141 (MQ=255)
                cagaCAGCGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGATTCAGACTCAGACAGCGACTCAGATTCAGAAAGAGATTCACATTCAGACAGCGaccccg                                                                                                                     >  2:242323/1‑136 (MQ=14)
                  gaCAGAGACGCAGAGTCAGATGGGGAGTCGGATTCGGACAGCGATTCAGACTCGGATAGCGACTCAGAGTCAGATAGCGATTCAGACTCAGACAGCGACTCAGATGCAGATAGCGATTCGGACTCAGACAGCGATTCAGAc                                                                                                                   <  2:159544/141‑1 (MQ=14)
                               attcagatAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGATAGCGATTCAGACTCAGATAGCGACTCAGACTCAGATAGCGATTCAGACTCAGACAGCGACTCAGACTCAGATAGCgacg                                                                                                      >  2:323908/1‑140 (MQ=11)
                                    gatAGCGACTCAGAGTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCgactcagac                                                                                                 <  1:387775/141‑1 (MQ=255)
                                            cTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGAGATACAGCCTCAGATAGCGAcccagactcggaagg                                                                                         >  2:396197/1‑138 (MQ=14)
                                             tCAGAGTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGc                                                                                        <  1:84999/141‑1 (MQ=255)
                                                 aTTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACt                                                                                    <  1:36136/141‑1 (MQ=255)
                                                    cgcaCAGCGATTCAGACAGAGATCGCGACTCAGATTCAGATAGCAATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCTGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACtcag                                                                                 <  1:10691/138‑1 (MQ=14)
                                                         aGCGAGTCAGACGCAGATATTGACGCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGACGCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACtcagattca                                                                            <  2:422698/141‑1 (MQ=14)
                                                          gCGATTCAGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGACTCAAATACGGAATCAGACCCAGAAATCGACtcagaaaccg                                                                           >  2:16146/1‑136 (MQ=11)
                                                            gATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGACTCAGATAGCGATTCAGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACtcagactccgat                                                                         >  2:114832/1‑141 (MQ=255)
                                                              ttCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAg                                                                       >  1:114238/1‑141 (MQ=255)
                                                               tCAGACTCAGATAGCGACTCAGATTAAGATAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGAGACCCGTACTCAGACCGCGATTCTGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGc                                                                      >  1:266504/1‑141 (MQ=14)
                                                                   aCTCAGATAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGAtt                                                                  >  1:354896/1‑141 (MQ=255)
                                                                      cAGATAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCgg                                                               <  1:83466/141‑1 (MQ=255)
                                                                          tAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGATTCAGACAGCGATTCAGACTCAGACAGCGAATCAGACTCAGATAGCGACTCAGACTCAGACCGCGACTCAGACACAGATAGCAACTCAGACTc                                                           >  2:298308/1‑141 (MQ=11)
                                                                                    gatacagatAGCGATTCAGACTCAGACAGCGACTCAGATTCAGAAAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGAc                                                 <  2:132466/141‑1 (MQ=255)
                                                                                      ttcagatAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTc                                               <  1:131041/141‑1 (MQ=255)
                                                                                         agatAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGAATAAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGa                                            >  1:117397/1‑141 (MQ=255)
                                                                                               cGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAGCGACTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGa                                      >  2:57303/1‑141 (MQ=255)
                                                                                                  ttCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACGCAGATTCAGACAg                                   >  1:125471/1‑141 (MQ=255)
                                                                                                    cagactcagacAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGACAGCg                                 >  1:393914/1‑141 (MQ=255)
                                                                                                        ggaggaaaGCGGCGCAGAGTCAGAAAGCGATGCGGACTCAGACAGCGATGCAGACTCAGAGAGCGACTCAGACTCAGACAGCGACGCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGACAGCGATTc                             <  2:184814/134‑1 (MQ=14)
                                                                                                        ctcagacAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGATTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGACAGCGATTc                             >  1:401430/1‑141 (MQ=255)
                                                                                                           agacAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGa                          >  1:341406/1‑141 (MQ=255)
                                                                                                           agaaAGCGAATGAGAGTGAGATAGAGATGGAGACTAAGAGAAGGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGa                          <  2:62656/141‑1 (MQ=14)
                                                                                                              cAGCGACTCAGATTCAGATAGAGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGACTc                       <  1:160911/141‑1 (MQ=255)
                                                                                                              aaGCGACACAGATTAAGAAAGATATTCAGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGATTCAGACTCAGACAGCGACTCAGattc                       <  2:202448/140‑4 (MQ=11)
                                                                                                               aGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGACTCa                      >  1:232952/1‑141 (MQ=255)
                                                                                                               aGCGAATCAGATTAAGATAGCGATTGAGACTAAAACAGCGATTCAGATTCAGATAGCGACTCAGACTCAGAAAGTGATTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGACTCa                      <  2:219778/141‑1 (MQ=14)
                                                                                                                 cGACTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGActcagactcaga                    >  2:394374/1‑141 (MQ=255)
                                                                                                                   aCTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGACTCAGATa                  <  1:316122/141‑1 (MQ=255)
                                                                                                                   aCTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGACTCAGATa                  >  1:44276/1‑141 (MQ=255)
                                                                                                                   aCTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGACTCAGATa                  >  1:417985/1‑141 (MQ=255)
                                                                                                                    ctgagattcagatAGCGATTCAGACTCAGACAGCGACTCAGACTAAGATGGTGAATCCGAGTCAGACAGCGATTCAGATTCAGATAGCGATTCCGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGACTCAGATAg                 <  2:374575/138‑1 (MQ=14)
                                                                                                                    cTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCCGATAGCGATTCCGACTCCGACAGcgactcagactcagacagcgactcagactcagacag                 >  2:341381/1‑141 (MQ=14)
                                                                                                                       atattcagatAGGGATTCGGACTCAGTCAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGACTCAGACAGCGACTCCGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGACTCAGATAGCga              <  2:124133/139‑1 (MQ=14)
                                                                                                                         agtcagatAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGACTCAGATAGCgact            <  1:151038/139‑1 (MQ=255)
                                                                                                                            cagatAGCGATTCGCACTTAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGATTCAGATTCAGACAGCGATTCAGACTCAGACAGCGACTCAGATTCAGACAGCGATTCAGACTCAGATAGCgactcag         <  2:294374/141‑1 (MQ=14)
                                                                                                                              gatAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTTAGACTCTTTCATCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGACTCAGATAGCgactcagac       >  1:16168/1‑141 (MQ=18)
                                                                                                                                tAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGACTCAGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGACTCTGATAGCgactcagactc     >  2:346336/1‑141 (MQ=255)
                                                                                                                                   cGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGACTCAGATAGCGActcaggctcaga  >  1:147556/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                      
GACAGTGATTCAGATTCAGACAGCGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGACTCAGATAGCGACTCAGACTCAGA  >  USA300TCH1516_ALE/622327‑622598

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: ‑