Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,433,396 C→T 18.1% A104V (GCA→GTA)  USA300HOU_RS12530 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,433,3960CT18.1% 67.5 / 8.0 35A104V (GCA→GTA) USA300HOU_RS12530hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (17/11);  new base T (3/3);  total (20/15)
Fisher's exact test for biased strand distribution p-value = 6.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.17e-01

CGAAAATCAAGTTTCCTATTATGAAATTATAACACTACTTAATAAACGTCCCCTCCGACAAGTCGACTATGGTAACAAAATTCAATATCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTACATAAATTATACAATTAAAAAGTTTCTTCAAATTGTAAAGATGCATTAATCGAGTTATAA  >  USA300TCH1516_ALE/2433268‑2433531
                                                                                                                                |                                                                                                                                       
cGAAAATCAAGTTTCCTATTATGAAATTATAACACTACTTAATAAACGTCCCCTCCGACAAGTCGACTATGGTAACAAAATTCAATATCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGc                                                                                                                             >  2:397195/1‑141 (MQ=255)
      tCAAGTTTCCTATTATGAAATTATAACACTACTTAATAAACGTCCCCTCCGACAAGTCGACTATGGTAACAAAATTCAATATCTTAATTTTTATCATACAGAACTATCTAACGCATAATTTGCAATTAAATTTGCCCATTa                                                                                                                       >  1:323732/1‑141 (MQ=255)
      tCAAGTTTCCTATTATGAAATTATAACACTACTTAATAAACGTCCCCTCCGACAAGTCGACTATGGTAACAAAATTCAATATCTTAATTTTTACCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGCCCATTa                                                                                                                       >  1:114305/1‑141 (MQ=255)
        aaGTTTCCTATTATGAAATTATAACACTACTTAATAAACGTCCCCTCCGACAAGTCGACTATGATAACAAAATTCAATCTCTTAATTTCTATCATACAGAATTATCTAGCGTATTAGTTGGAATTAGAGTTGCCCAGTAAc                                                                                                                     <  2:114428/141‑1 (MQ=255)
          gTTTCCTATTATGAAATTATAACACTACTTAATAAACGTCCCCTCCGACAAGTCGACTATGGTAACAAAATTCAATATCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGCCCATTAACCt                                                                                                                   <  1:371331/141‑1 (MQ=255)
          gTTTCCTATTATGAAATTATAACACTACTTAATAAACGTCCCCTCCGACAAGTCGACTATGGTAACAAAATTCAATATCTTAATTTTTATCATACAGAACTACCTAACGCATTATTTGCAATTAAATTTGCCCGTTAACCt                                                                                                                   >  2:178573/1‑141 (MQ=255)
               cTATTATGAAATTATAACACTACTTAATAAACGTCCCCTCCGACAAGTCGACTATGGTAACAAAATTCAATATCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTCCCCATTAACCTAtttt                                                                                                              >  1:155492/1‑141 (MQ=255)
                         aTTATAACACTACTTAATAAACGTCCCCTCCGACAAGTCGACTATGGTAACAAAATTCAATATCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGTAATTAAATTTGCCCATTAACCTATTTTTCATAAAATg                                                                                                    >  1:163110/1‑141 (MQ=255)
                         aTTATAACACTACTTAATAAACGTCCCCTCCGACAAGTCGACTATGGTAACAAAATTCAATATCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGTAATTAAATTTGCCCATTAACCTATTTTTCATAAAATg                                                                                                    >  2:311517/1‑141 (MQ=255)
                         aTTATAACACTACTTAATAAACGTCCCCTCCGACAAGTCGACTATGGTAACAAAATTCAATATCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGTAATTAAATTTGCCCATTAACCTATTTTTCATAAAATg                                                                                                    >  2:136205/1‑141 (MQ=255)
                           tataACACTACTTAATAAACGTCCCCTCCGACAAGTCGACTATGGTAACAAAATTCAATATCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGCCAATTAACCTATTTTTCATAAAATGTc                                                                                                  >  2:120440/1‑141 (MQ=255)
                            ataACACTACTTAATAAACGTCCCCTCCGACAAGTCGACTATGGTAACAAAATTCAATATCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCa                                                                                                 <  2:389202/141‑1 (MQ=255)
                              aaCACTACTTAATAAACGTCCCCTCCGACAAGTCGACTATGGTAACAAAATTCAATATCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCAtt                                                                                               >  2:307898/1‑141 (MQ=255)
                                       taataaACGTCCCCTCCGACAAGTCGACTATGGTAACAAAATTCAATATCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCCTTTACACaaat                                                                                      >  2:102782/1‑139 (MQ=255)
                                       taataaACGTCCCCTCCGACAAGTCGACTATGGTAACAAAATTCAATATCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGt                                                                                      >  1:182451/1‑141 (MQ=255)
                                                 ccccTCCGACAAGTCGACTATGGTAACAAAATTCAATATCTTACTTTTTATCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTaa                                                                            <  1:230428/141‑1 (MQ=255)
                                                                     tGGTAACAAAATTCACTATCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTACATaaa                                                        <  1:10749/141‑1 (MQ=255)
                                                                       gTAACAAAATTCAATATCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTACATAAAtt                                                      <  2:365467/141‑1 (MQ=255)
                                                                               actCAATATCTTAATTTTTATCATACAGAACTATCTAGCGCATTATTTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTACATAAATTATACAAtt                                              <  1:50617/139‑1 (MQ=255)
                                                                               aTTCAATATCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTACAATCAACTTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTATATAAATTATACAAtt                                              <  1:294389/141‑1 (MQ=255)
                                                                                 tCAATATCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAACTGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTACATAAATTATACAATTaa                                            >  1:123368/1‑141 (MQ=255)
                                                                                    atatCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTACATAAATTATACAATTaaaaa                                         >  1:137081/1‑141 (MQ=255)
                                                                                     tatCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTACATAAATTATACAATTAAAAAg                                        >  1:322264/1‑141 (MQ=255)
                                                                                      atCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTCCATAAATTATACAATTAAAAAGt                                       >  1:6976/1‑141 (MQ=255)
                                                                                      atCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTACATAAATTATACAATTAAAAAGt                                       <  2:322264/141‑1 (MQ=255)
                                                                                                  aTCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTACATAAATTATACAATTAAAAAGTTTTTTCAAAttt                           >  2:10294/1‑140 (MQ=255)
                                                                                                         aGAACTATCTAACGCATTATTTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTACATAAATTATACAATTAAAAAGTTTCTTCAAATTGTAAAGAt                    >  1:323349/1‑141 (MQ=255)
                                                                                                             cTATCTAACGCATTATTTGCAATTAAATTTTCCTATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTACATAAATTATACAATTAAAAAGTTTCTTCAAATTGTAAAGATGCAt                <  2:287420/141‑1 (MQ=255)
                                                                                                                    aCGCATCGTTTGCAATTAAATTTGCCAATTAATAGAATTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTACATAAATTATACAATTAAAAATTTTCTTCAAATTGTAAAGATGCATTAATCGa         <  2:20654/141‑1 (MQ=255)
                                                                                                                        attattTGTAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTACATAAATTATACAATTAAAAAGTTTCTTCAAATTGTAAAGATGCATTAATCGAGTta     <  1:311517/141‑1 (MQ=255)
                                                                                                                        attattTGTAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTACATAAATTATACAATTAAAAAGTTTCTTCAAATTGTAAAGATGCATTAATCGAGTta     <  2:163110/141‑1 (MQ=255)
                                                                                                                        attattTGTAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTACATAAATTATACAATTAAAAAGTTTCTTCAAATTGTAAAGATGCATTAATCGAGTta     <  1:136205/141‑1 (MQ=255)
                                                                                                                           attTGCAATTAAATTTGCCCATTAACCTATTTTTCATACAATGTCATTTAAACAAGTTCTTTATTACAATTCACTTTATTACCTAAATTATCCAATTAAAAAGTTTCTTCAAATTGTACAGATGCATTAATCACGTCATaa  >  2:171356/1‑141 (MQ=255)
                                                                                                                           attTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTACATAAATTATACAATTAAAAAGTTTCTTCAAATTGTAAAGATGCATTAATCGAGTTATaa  <  2:182451/141‑1 (MQ=255)
                                                                                                                           attTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTACATAAATTATACAATTAAAAAGTTTCTTCAAATTGTAAAGATGCATTAATCGAGTTATaa  >  2:344956/1‑141 (MQ=255)
                                                                                                                                |                                                                                                                                       
CGAAAATCAAGTTTCCTATTATGAAATTATAACACTACTTAATAAACGTCCCCTCCGACAAGTCGACTATGGTAACAAAATTCAATATCTTAATTTTTATCATACAGAACTATCTAACGCATTATTTGCAATTAAATTTGCCCATTAACCTATTTTTCATAAAATGTCATTTAAACAAGTTATTTATTAAAATTCACTTTATTACATAAATTATACAATTAAAAAGTTTCTTCAAATTGTAAAGATGCATTAATCGAGTTATAA  >  USA300TCH1516_ALE/2433268‑2433531

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑