Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 459,019 G→A 7.7% G27E (GGG→GAG)  USA300HOU_RS02175 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE459,0190GA 7.7% 134.5 / 2.5 52G27E (GGG→GAG) USA300HOU_RS02175hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (15/33);  new base A (2/2);  total (17/35)
Fisher's exact test for biased strand distribution p-value = 5.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.15e-01

ATCGCAGAAATTGAGCAAGAAATCAATGCATACCTGAAAGAACTTGGGGTGTTGAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAAATCAGTTTCGTCGAAAAATCTAGAAAATTA  >  USA300TCH1516_ALE/458882‑459157
                                                                                                                                         |                                                                                                                                          
aTCGCAGAAATTGAGCAAGAAATCAATGCATACCTGAAAGAACTTGGGGTGTTGAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAgggg                                                                                                                                          >  1:33581/1‑140 (MQ=38)
   gCAGAAATTGAGCAAGAAATCAATGCATACCTGAAAGAACTTGGGGTGTTGAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATc                                                                                                                                       <  2:246662/140‑1 (MQ=255)
     aGAAATTGAGCAAGAAATCAATGCATACCTGAAAGAACTTGGGGTGTTGAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCtt                                                                                                                                     <  1:515595/140‑1 (MQ=255)
     aGAAATTGAGCAAGAAATCAATGCATACCTGAAAGAACTTGGGGTGTTGAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCtt                                                                                                                                     <  2:425378/140‑1 (MQ=255)
      gAAATTGAGCAAGAAATCAATGCATACCTGAAAGAACTTGGGGTGTTGATAGATGAGTAATACACAAAAGACAAAGGTGCCAGAATTTAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTa                                                                                                                                    <  2:359187/140‑1 (MQ=255)
      gAAATTGAGCAAGAAAACAATGCATACCGGAAAGAACTTGGGGTGTTGAAAGATGAGTAAGACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGCGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTa                                                                                                                                    <  2:303145/140‑1 (MQ=255)
      gAAAGTGAGCAAGAAATCAATGCATACCTGAAAGAACTTGGGGTGTTGAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTa                                                                                                                                    <  2:313479/140‑1 (MQ=255)
       aaaTTGCGCAAGAAATCAATGCATACCTGAAAGAACTTGGGGTGTTGAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTAc                                                                                                                                   <  1:197744/140‑1 (MQ=255)
          ttGAGCAAGAAATCAATGCATACCTGAAAGAACTTGGGGTGTTGAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGa                                                                                                                                <  2:452302/140‑1 (MQ=255)
                      tCAATGCATACCTGAAAGAACTTGGGGTGTTGAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGATATGAAGGCGAAAGGGAAGAGAAGCAGATAGGGGATCTTACAGATAGAGTAATTAg                                                                                                                    >  1:47909/1‑140 (MQ=255)
                        aaTGCATACCTGAAAGAACTTGGGGTGTTGAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGAGGATCTTACAGATAGAGTAATTAGGa                                                                                                                  >  1:63567/1‑140 (MQ=255)
                        aaTGCATACCTGAAAGAACTTGGGGTGTTGAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGAGGATCTTACAGATAGAGTAATTAGGa                                                                                                                  >  1:63511/1‑140 (MQ=255)
                          tGCCTACCTGAAAGAATCTGGGGTGTTGAAAGAAGATTAATACACAAAAGAAAAATGTGGCAGAATTGAGGTTCCCAGGGTTTGCAGGCGAATGGGAAGAGAATCAGTTAGGGTGTCTTACATATAGAGTAATTCGGaaa                                                                                                                <  2:278583/140‑1 (MQ=17)
                          tGCATACCTGAAAGAACTTGGGGTGTTGAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGaaa                                                                                                                <  2:499462/140‑1 (MQ=255)
                                        aaCTTGGGGTGTTGAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGa                                                                                                  >  1:420663/1‑140 (MQ=255)
                                             ggggTGTTGAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGa                                                                                             >  1:187752/1‑140 (MQ=255)
                                                gtgtTGAAAGATGAGTAATACACAAAAGAAAACTGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTGACAGATAGAGTAAGTAGGAAAACTAAAAACTTAGAATCGaaaa                                                                                          >  2:108006/1‑140 (MQ=255)
                                                gtgtTGAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCTCCGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGTGATCTTACAGATAGAGTAATTAGGAAAATTAAAAACTTAGAATCGaaaa                                                                                          <  2:302315/140‑1 (MQ=255)
                                                gtgtTGAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATAAGGAAAAATCAAAACTTAGAATCGaaaa                                                                                          >  1:63466/1‑140 (MQ=255)
                                                gtggtgAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGaaaa                                                                                          <  2:513608/140‑1 (MQ=255)
                                                    tGAAAGATGAGTAATACACAAAGTGAAAAGGGTCCTGGATTGTCGATATAAAACTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGcc                                                                                      <  1:536402/140‑1 (MQ=25)
                                                    tGAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAAAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGcc                                                                                      >  1:7434/1‑140 (MQ=255)
                                                           tGAGTAATACACAAAAGAAAAATGTGCCACATTTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGTAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACa                                                                               <  1:281735/140‑1 (MQ=255)
                                                                 aaaaacaAAAAAAAAAAGTTCCAGAAATAATCTGCCCAGTGATTGAAGGCGAATGCCAAGAGAAGCAGTTAGGGAATCATACAGATAGCGTAATTACGAAAAATAAAAAAAAAAAAAAAAAAAAGCCTTTAACAATATcc                                                                         <  2:101272/136‑1 (MQ=255)
                                                                    cacaAAAGAAAAATGGGCCAGAATTGAGATTCCCAGGGTGTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAACAGCCTTTAACAATATCCGGa                                                                      <  2:164614/140‑1 (MQ=255)
                                                                      caAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACa                                                                    <  1:24047/140‑1 (MQ=255)
                                                                        aaaGAAAAATGTTCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGATTAATTAGGACAAATAATAACTTAGAATCAAAAAAGCCTTTAACAATTTCCGGACAGt                                                                  <  2:423551/140‑1 (MQ=25)
                                                                          aGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAAACGAAAAAGCCTTTAACAATATCCGGACAGTTa                                                                >  1:7292/1‑140 (MQ=255)
                                                                            aaaaaTGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTATGAAAAATAAAAACTTAGAATCAAAAAAGCCTTTAACAATATCCGGACAGTTAga                                                              >  1:134112/1‑139 (MQ=255)
                                                                                  gtgCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATGGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAAt                                                        >  2:295479/1‑140 (MQ=255)
                                                                                    gCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGATTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTg                                                      <  1:504434/140‑1 (MQ=255)
                                                                                     ccAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGa                                                     >  2:29276/1‑140 (MQ=255)
                                                                                     ccAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGa                                                     <  1:488690/140‑1 (MQ=255)
                                                                                       aGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTGTAATTGATc                                                   >  1:483750/1‑140 (MQ=255)
                                                                                       aGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGAGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGATc                                                   <  2:63567/140‑1 (MQ=255)
                                                                                       aGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGAGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGATc                                                   <  2:63511/140‑1 (MQ=255)
                                                                                        gAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGATCa                                                  >  2:209957/1‑140 (MQ=255)
                                                                                        gAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGATCa                                                  >  2:503007/1‑140 (MQ=255)
                                                                                             gAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGTGTAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGATCAAACAg                                             <  1:41456/140‑1 (MQ=255)
                                                                                             gAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGATCAAACAg                                             <  1:21647/140‑1 (MQ=255)
                                                                                             gAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAAGCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGATCAAACAg                                             <  1:221276/140‑1 (MQ=255)
                                                                                                    cccgggTTGTAAGGCGAATGGGAAAAGAAGGAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGATCAAACAGAATAttt                                      <  2:128106/137‑1 (MQ=255)
                                                                                                            tGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAAAt                              <  1:19898/140‑1 (MQ=255)
                                                                                                                    aaTGGGAAGAGAAGCAGTTAGGGGATCGTACAGATAGAGTAAATAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAAATCAGTTtcg                      <  2:47909/140‑1 (MQ=255)
                                                                                                                      tGGGAAGAGACGCAGTAAGGGGATCTTACAGATAGGGGAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCGTTAACAATCGCCGGACAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAAATTAGTTtcgtc                    <  2:265603/140‑1 (MQ=255)
                                                                                                                      tGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGCCAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAAATCAGTTtcgtc                    <  1:364747/140‑1 (MQ=255)
                                                                                                                         gAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAAATCAGTTTCGTCGaa                 >  1:294043/1‑140 (MQ=255)
                                                                                                                               aaGCTGTTAGGGGATCTTACAGATAGAATAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAAATCAGTTTCGTCGAAAAATCt           <  2:394685/140‑1 (MQ=255)
                                                                                                                               aaGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAAATCAGTTTCGTCGAAAAATCt           <  1:350861/140‑1 (MQ=255)
                                                                                                                                    gTTAGGGTATCTTACAGATAGAGTAATTAGGAAATATAAAAACTTAGCATCGAAAAACCCTTTAACACTATCCGGACAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAAATCAGTTTCGTCGAAAAATCTAGaaa      <  2:429740/140‑1 (MQ=255)
                                                                                                                                    gTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAGAAAAGTTTCGTCGAAAAATCTAGaaa      <  1:544334/140‑1 (MQ=255)
                                                                                                                                    gTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAAATAAGTTTCGTCGAAAAAACTAGaaa      >  1:506051/1‑140 (MQ=255)
                                                                                                                                     ttAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGTCTTTAACAATATCCGGACAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAAATCAGTTTCGTCGAAAAATCTAGaaaa     <  1:304080/140‑1 (MQ=255)
                                                                                                                                        gggtATTTTACAGATAGAGTAATTAGGAAAACTAAAATTTCAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAAATCAGTTTCGTCGAAAAATCTAGAAAATta  <  1:372552/140‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                          
ATCGCAGAAATTGAGCAAGAAATCAATGCATACCTGAAAGAACTTGGGGTGTTGAAAGATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGTTTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAGTAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAAATCAGTTTCGTCGAAAAATCTAGAAAATTA  >  USA300TCH1516_ALE/458882‑459157

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: ‑