Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,775,439 C→T 49.7% G362D (GGT→GAT)  clpX ← ATP‑dependent Clp protease ATP‑binding subunit ClpX

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,775,4390CT49.7% 2.1 / 30.7 26G362D (GGT→GAT) clpXATP‑dependent Clp protease ATP‑binding subunit ClpX
Reads supporting (aligned to +/- strand):  ref base C (9/4);  new base T (6/7);  total (15/11)
Fisher's exact test for biased strand distribution p-value = 4.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTATAGTTCTGGTTCAGTTTCTTCATTAATTGTTTGTGCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAGGTTGCGTTAAGATGT  >  USA300TCH1516_ALE/1775305‑1775571
                                                                                                                                      |                                                                                                                                    
cgtATAGTTCTGGTTCAGTTTCTTCATTAATTGTTTGTGCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGttt                                                                                                                                <  2:5289/141‑1 (MQ=255)
     aGTTCTGGTTCAGTTTCTTCATTAATTGTTTGTGCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATTATTGAACGTAAACCACGCGCACCTGTTtttctt                                                                                                                           <  1:196416/141‑1 (MQ=255)
      gTTCTGGTTCAGTTTCTTCATTAATTGTTTGTGCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGTTtttcttt                                                                                                                          >  1:168848/1‑141 (MQ=255)
        tCTGGTTCAGTTTCTTCATTAATTGTTTGTGCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCa                                                                                                                        <  2:125344/141‑1 (MQ=255)
                                  ttgtGCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATaa                                                                                              >  2:333082/1‑141 (MQ=255)
                                   tgtgCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATaaa                                                                                             <  2:18022/141‑1 (MQ=255)
                                   tgtgCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATaaa                                                                                             >  2:135872/1‑141 (MQ=255)
                                     tgCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGc                                                                                           <  2:99597/141‑1 (MQ=255)
                                               aCTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTg                                                                                 <  2:320267/141‑1 (MQ=255)
                                                        gTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTaaa                                                                        >  1:65290/1‑141 (MQ=255)
                                                         ttACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAAt                                                                       <  2:324481/141‑1 (MQ=255)
                                                              ttttCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCcaca                                                                  >  1:13642/1‑141 (MQ=255)
                                                                  cgaaaGAAGGCACATCAAACATAGTAGCGATCAACGAGACATCTCTGATTGTACGTCAACCACGCGCATCTGTTTTTCTCTCAATTGCTTTCTCACTAATTGCTGATAAAGCTTCTTCAGTCAACTCTAAATCCAcatcat                                                              >  2:37563/5‑141 (MQ=255)
                                                                        aaGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAAtt                                                        >  1:285221/1‑141 (MQ=255)
                                                                        aaGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAGGCTTCTTCAGTGAACTCTAAATCCACATCATCTAAtt                                                        <  2:121928/141‑1 (MQ=255)
                                                                          ggCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTcc                                                      <  2:241033/141‑1 (MQ=255)
                                                                            cacaTCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCGTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAg                                                    >  2:199888/1‑141 (MQ=255)
                                                                              caTCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCa                                                  >  1:152052/1‑141 (MQ=255)
                                                                                        aataTCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGtata                                        >  1:85559/1‑141 (MQ=255)
                                                                                             cGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGtt                                   >  2:109929/1‑141 (MQ=255)
                                                                                              gATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCTCTTATTTTTGATAAAGCTTCTTCAGTTAACTCTAAATCCACATCATCTAATTCCAGCCTTTTGGTATATTGctt                                  >  2:187087/1‑141 (MQ=255)
                                                                                                ttAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTca                                <  1:360185/141‑1 (MQ=255)
                                                                                                 tAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTcac                               >  2:331637/1‑141 (MQ=255)
                                                                                                       ttcttcTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGc                         >  1:240776/1‑141 (MQ=255)
                                                                                                                gATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAgg                <  2:152052/141‑1 (MQ=255)
                                                                                                                              cACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAGGTTGCGTTAAGATGt  >  2:326272/1‑141 (MQ=255)
                                                                                                                                      |                                                                                                                                    
CGTATAGTTCTGGTTCAGTTTCTTCATTAATTGTTTGTGCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAGGTTGCGTTAAGATGT  >  USA300TCH1516_ALE/1775305‑1775571

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