Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,352,815 G→A 11.4% A92V (GCA→GTA)  rpsI ← 30S ribosomal protein S9

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,352,8150GA11.4% 136.5 / 3.3 55A92V (GCA→GTA) rpsI30S ribosomal protein S9
Reads supporting (aligned to +/- strand):  ref base G (31/16);  new base A (5/2);  total (37/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

ATATCGTCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTCTAAAATTAA  >  USA300TCH1516_ALE/2352677‑2352954
                                                                                                                                          |                                                                                                                                           
atatCGTCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCt                                                                                                                                           <  1:319248/141‑1 (MQ=255)
  atCGTCCGACAATTACCGTTTTGAGAATAGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAAAGCGTTTTAAAGACCCTCTGTATTCAGGATCGTCTTc                                                                                                                                         >  2:134322/1‑141 (MQ=37)
  atCGTCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTc                                                                                                                                         >  1:5333/1‑141 (MQ=255)
       ccGACAATTAACGTTTTGAGTATCGAGGTGAACGAGGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTATATTCAGGATCTACTTCtaata                                                                                                                                    >  2:68970/1‑141 (MQ=38)
          aCAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATg                                                                                                                                 <  1:516861/141‑1 (MQ=255)
          aCAATTAACGTTTTGAGAAATGAGGAGAACGACGAGCTGCTTTAGGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATg                                                                                                                                 >  1:335157/1‑141 (MQ=255)
           cAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGc                                                                                                                                >  1:339193/1‑141 (MQ=255)
            aaTTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCa                                                                                                                               >  2:200333/1‑141 (MQ=255)
              ttAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACg                                                                                                                             >  1:23795/1‑141 (MQ=255)
                aaCGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCAGTATTCAGGGTCTGCTTCTAATAATGCACGAg                                                                                                                           >  1:45883/1‑141 (MQ=255)
                  cGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCAACTTCTATTAATGCACGAGCg                                                                                                                         >  1:380736/1‑141 (MQ=255)
                   gTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGGTCTGCGTCTAATAATGCACGAGCGa                                                                                                                        >  1:379070/1‑141 (MQ=255)
                     tttGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGAtt                                                                                                                      >  1:528735/1‑141 (MQ=255)
                              tGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGTTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAAACTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACgg                                                                                                             <  1:19454/141‑1 (MQ=255)
                                  gTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATag                                                                                                         >  1:539650/1‑141 (MQ=255)
                                  gTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATag                                                                                                         <  1:386732/141‑1 (MQ=255)
                                   tGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATagc                                                                                                        >  1:190885/1‑141 (MQ=255)
                                           gaGCTGCTTTAAGACGTGGGTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgagctt                                                                                                >  1:455727/1‑141 (MQ=255)
                                           gaGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgagctt                                                                                                >  2:35376/1‑141 (MQ=255)
                                             gctgctTGTAGAGCTGTTTTTGTACGTTCTTTCCAACCTGGGTCACGAGTAAGTGATCCAGCGCTGTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATGATGCATGAGCGATTCCGTTACGGATAGCTTGAGCTTGt                                                                                              <  1:342060/141‑1 (MQ=255)
                                               tgctTTAAGACCTGGTTTTTTTTTTTTTTTTTTACGTGGGTCACGAGTAAGTAATTTAGCGCGTTTTAAAGAACCTCTGTATTCGGGATCTGCTTCTAATAATGCACGAGCGATTCCGTTACGGATAgcttgtgcttgttt                                                                                            >  2:443766/1‑139 (MQ=255)
                                                     aaGACCTGGTTTTTTACGTTCTTTCATACTGGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGaa                                                                                      <  2:552675/141‑1 (MQ=255)
                                                      aGACCTGTTTTTTTACGTCCTTTCATACGGGGGGCACGAGTACGTCTAGGCCCCCTTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGaaa                                                                                     <  1:288902/141‑1 (MQ=255)
                                                      aGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGaaa                                                                                     >  2:190158/1‑141 (MQ=255)
                                                         ccTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccc                                                                                  >  1:38328/1‑140 (MQ=255)
                                                            ggTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccacca                                                                               >  1:157943/1‑141 (MQ=255)
                                                             gTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGTTTGAGCTTGTCCAGTGAAaccaccac                                                                              <  2:366955/141‑1 (MQ=255)
                                                              ttttttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccaccacc                                                                             >  1:561657/1‑141 (MQ=255)
                                                                 tttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTCTTCCAGTGTAACCACCACCATg                                                                          >  1:47090/1‑141 (MQ=255)
                                                                  ttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACCGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGa                                                                         >  2:236003/1‑141 (MQ=255)
                                                                    aCGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAAc                                                                       >  1:173882/1‑141 (MQ=255)
                                                                     cGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACg                                                                      <  1:542675/141‑1 (MQ=255)
                                                                          ttccATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAAc                                                                 <  2:594862/138‑1 (MQ=255)
                                                                           ttCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACt                                                                >  1:67421/1‑141 (MQ=255)
                                                                           ttCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACt                                                                >  2:421768/1‑141 (MQ=255)
                                                                               tACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTaaaa                                                            >  2:459794/1‑141 (MQ=255)
                                                                                   tGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAACAAAACACCTTGAACGTTAACTAAAAcgtc                                                        >  2:456090/1‑141 (MQ=255)
                                                                                    gggTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAcatca                                                       >  1:37701/1‑141 (MQ=255)
                                                                                     ggTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAcatcaa                                                      >  1:241903/1‑140 (MQ=255)
                                                                                           gAGTAAGTAATCCAGCGCGTTTTAAAGACCCTCTGTATTCAGGATCTGCTTCTAATAATGCTCGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAGGTAAGACATCATAGTCAc                                                >  1:115495/1‑141 (MQ=255)
                                                                                              taagtaaTCCAGCGCGTTTTAAAGAAACTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCtt                                             >  2:587084/1‑141 (MQ=255)
                                                                                                  taaTCCAGCCCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGt                                         <  1:219189/141‑1 (MQ=255)
                                                                                                     tcaaGCGCGTTTTAAAGAACCTCTGTATTCAGCGTCTGCTTCTAATAATGCACGAGCGATTCGGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCCCGATGAACGTTAACGAAAACATCGTAGTTACCTTTAGTTTc                                      >  1:208377/4‑141 (MQ=255)
                                                                                                         gcgcGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGtt                                  <  1:35376/141‑1 (MQ=255)
                                                                                                           gcgTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTAc                                >  1:471790/1‑141 (MQ=255)
                                                                                                           gcgTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTAc                                <  2:67421/141‑1 (MQ=255)
                                                                                                                    aGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAAtgg                       <  1:200333/141‑1 (MQ=255)
                                                                                                                    aGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAAtgg                       <  1:459794/141‑1 (MQ=255)
                                                                                                                        ccTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAAtggttgg                   >  1:161512/1‑141 (MQ=255)
                                                                                                                                ttCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTc           <  2:561657/141‑1 (MQ=255)
                                                                                                                                 tCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCATTTACATCAAATGGTTGGTTTAAGTCt          <  2:157943/141‑1 (MQ=255)
                                                                                                                                  cAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTGGGTTTAAGTCTa         >  1:45931/1‑141 (MQ=255)
                                                                                                                                   aGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGGTAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAAGGGTTGGTTTAAGTCTaa        >  1:4287/1‑141 (MQ=255)
                                                                                                                                      aTCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTCTAAAAt     <  1:459184/141‑1 (MQ=255)
                                                                                                                                         tGCTTCTAATAATGCACGAGCGATTCCGTGCCGGATAGCTCGAGCAAGACCTGGTACACCACCACCATGAACGTTAACTAAAACATCATAGTTACCCTTAGCTTCAGTTACATAAAATCGCTGGTCTAACACTCAAAttct  >  2:128836/1‑139 (MQ=255)
                                                                                                                                          |                                                                                                                                           
ATATCGTCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTCTAAAATTAA  >  USA300TCH1516_ALE/2352677‑2352954

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: ‑