Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,028,508 A→T 22.2% V46E (GTA→GAA)  USA300HOU_RS10230 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,028,5080AT22.2% 91.3 / 11.4 43V46E (GTA→GAA) USA300HOU_RS10230hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (14/19);  new base T (6/4);  total (20/23)
Fisher's exact test for biased strand distribution p-value = 4.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAACGCACAATAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTC  >  USA300TCH1516_ALE/2028370‑2028642
                                                                                                                                          |                                                                                                                                      
tAACGCACAATAAGTAATAATAAAAAAACTAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGAAATAAATATCGCGCCTATCCAAAAAGACAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTAc                                                                                                                                       <  2:239988/140‑1 (MQ=255)
   cGCACAATAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAACAGGCCACGTATTTTATGAAAATAAAGATCTcctaccta                                                                                                                                    >  1:244317/1‑140 (MQ=255)
   cGCACAATAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATa                                                                                                                                    >  1:206175/1‑140 (MQ=255)
          ttaataaaaaaaaAAAGACGAACAAGATGATCATTGTATACTTATTACACAATAATGTGAATGCAATTAATATCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAAt                                                                                                                             <  2:153465/136‑1 (MQ=255)
          tAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCACAAGGCCACGTATTTTATGAAAATAAAGATATCCTTCATAAACTAAt                                                                                                                             >  1:574826/1‑140 (MQ=255)
          tAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCCCGTATTTTATGAAAATACAGATATCCTTCATAAACCAAt                                                                                                                             >  1:28352/1‑140 (MQ=255)
          tAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAAt                                                                                                                             <  2:301523/140‑1 (MQ=255)
          tAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAAt                                                                                                                             <  2:409732/140‑1 (MQ=255)
                ataataaAAAGACGAACAAGAGGATGATTGTATACTTATTAGACAATAATGTGAATTCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACAt                                                                                                                       <  2:132440/140‑1 (MQ=255)
                    taaAAAGACGAACAAGATGATTATTGTAGACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCa                                                                                                                   <  1:439300/140‑1 (MQ=255)
                         aGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTCTGAAAATAAAGATATCCTACATAAACTAATACACAACCCaataat                                                                                                              >  2:447479/1‑140 (MQ=255)
                         aGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCaataat                                                                                                              >  1:452959/1‑140 (MQ=255)
                               aCAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACg                                                                                                        <  1:632349/140‑1 (MQ=255)
                                        tgatTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAg                                                                                               <  2:206175/140‑1 (MQ=255)
                                        ggatCGTATACTTATTGAACAACAACGTGAATGCAATTAATAGGGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAg                                                                                               <  2:244317/139‑1 (MQ=255)
                                         gatTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGc                                                                                              <  1:672501/140‑1 (MQ=255)
                                                     attaAACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCaa                                                                                  <  1:379498/140‑1 (MQ=255)
                                                       taGACCAAAATGAGAATTGAATTAATAGTGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATAACCTTCATAAACTAATATACATCACAATAATAGAACGAGTAAAAAGCCAATTTTTTCaaaa                                                                                <  2:575931/140‑1 (MQ=255)
                                                       taGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTTCATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCaaaa                                                                                <  1:408680/140‑1 (MQ=255)
                                                           taacaatGTGAACGCAATTAATAGCGCGCTGATCCAAAACACCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTACTACACATCCCAATAATAGAACGAGTAAAAAGCCTATTTTTTCAAAAAata                                                                            <  2:67743/136‑1 (MQ=255)
                                                           cAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAata                                                                            >  2:336210/1‑140 (MQ=255)
                                                            aataatGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTTCATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAatat                                                                           >  2:100006/1‑140 (MQ=255)
                                                            aataatGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTTCATAAACTAATACACATACCAGTAATAGAACGCGTAAAAAGCCAATTTTTTCaaaacacat                                                                           >  1:196373/1‑135 (MQ=255)
                                                                gtgtgAGGGCAATGTAGAGCGGGGCTATCCGAGACGCCAAAAGGCGACGTATTTGATGAAAATAAAGATATCCTACATAAACTAATACGCATCCCAAGAAGAGGAGGAGTAAAGAGCCAAGTTTTGCAAAAAATATgtag                                                                       <  2:323703/139‑1 (MQ=255)
                                                                 tgtgAATGCAATCAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATTCACATCCCAATAATAGCACGAGTAAAAAGCCAATTTTTTCAAAAAATATgtagt                                                                      <  2:92996/140‑1 (MQ=255)
                                                                  gtgAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTTCATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATgtagta                                                                     >  1:519713/1‑140 (MQ=255)
                                                                  gggAATGTAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATATACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATgtagta                                                                     <  2:323058/138‑1 (MQ=255)
                                                                     agtGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCAAATTTTTTCAAAAAATATGTAGTaaaa                                                                  >  2:476517/3‑140 (MQ=255)
                                                                                tAGCGCGCCTATCCAAACCGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAACCCAATCTTTTCCAAAAATCTGGAGTAAAAATTgcacataa                                                       >  2:694588/1‑133 (MQ=255)
                                                                                tAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATACACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATAGGTCGTAACGATTGGCaataa                                                       >  1:141130/1‑140 (MQ=255)
                                                                                tAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAGGCCCATTTTTTCAAAAAATATGTAGTAGAAATTGGCaaaaa                                                       >  1:223903/1‑140 (MQ=255)
                                                                                tAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCATCAAATATGGAGTAAAAATTGGCaataa                                                       >  2:111110/1‑140 (MQ=255)
                                                                                tAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCaataa                                                       <  2:335132/140‑1 (MQ=255)
                                                                                             cAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGt                                          >  1:178745/1‑140 (MQ=255)
                                                                                               aaaCGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTaa                                        >  2:650809/1‑140 (MQ=255)
                                                                                                 aCGCCAAAAGGCCACGTATTTTCTGAAAATAAAGATATCCCTCATCAACTAATACACATCCCAATAATAGAACCAGTAAAAACCCAATTTCTTCAAACCATATGTCGTAACAATCAGCCATAATCATTAATGCGGTcaaa                                      >  2:140070/1‑140 (MQ=255)
                                                                                                   gCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAAt                                    >  2:453802/1‑140 (MQ=255)
                                                                                                            ccACTTATTTTATGAAAATAAAGATATCCTTCATAAACTAATACACATCCCAATAATAGAACGAGTAAATAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACAt                           <  2:294565/140‑1 (MQ=255)
                                                                                                            ccACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACAt                           <  2:178745/140‑1 (MQ=255)
                                                                                                             cACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGCAAAAAGCCAATTTTTTCACAATATATGTAGGTCAGATGAGCAATAATCATTAATGCAGTAAAAATGATCAACagt                          >  2:312546/1‑138 (MQ=255)
                                                                                                              aCGTCTTTTATGACAATAAAGATATCCTTCATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGGAAAAATGATCAACAttt                         <  2:550498/140‑1 (MQ=255)
                                                                                                              aCGTATTTTATTAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATTTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACAttt                         <  2:353375/140‑1 (MQ=255)
                                                                                                                     ttATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGa                  >  2:427188/1‑140 (MQ=255)
                                                                                                                                     atCCAACATAAACAAATACAAAGGAAAATAATAGAACGATTAAAAAGCAAAAAAAAAAAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTc  <  2:398154/140‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                      
TAACGCACAATAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTC  >  USA300TCH1516_ALE/2028370‑2028642

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: ‑