Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,892,051 A→T 8.4% intergenic (‑144/+376) rot ← / ← USA300TCH1516_01749 HTH‑type transcriptional regulator rot/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,892,0510AT 8.4% 126.7 / 5.5 49intergenic (‑144/+376)rot/USA300TCH1516_01749HTH‑type transcriptional regulator rot/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (26/18);  new base T (2/2);  total (29/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.76e-01

ACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAACAAATCACTCTATTACATATTAATTTTATAATTTATATACAAAGAAAATATATCAATATTAC  >  USA300TCH1516_ALE/1891913‑1892191
                                                                                                                                          |                                                                                                                                            
aCATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGt                                                                                                                                            <  2:584231/141‑1 (MQ=255)
     tcCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACATCACAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAACAAACTTACTTTCTATTAAATTCTCACAGTTGAAt                                                                                                                                       >  2:359588/1‑141 (MQ=255)
         aaTTAATAATCACATATTTAGCTACTATATTAGTATTAATAAACATCCCATCAATTCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATaaaa                                                                                                                                   <  1:37229/141‑1 (MQ=255)
           ttAATAATCAAATAATTAGCTACTAGATGAGTATTAACAAATATACAAACAATCTCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAAGTGTCAATGTTGAATAAAAtt                                                                                                                                 <  2:265018/141‑1 (MQ=255)
            taataaTCACATATTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTATCAAAGTTGAATAAAATTa                                                                                                                                >  2:459231/1‑141 (MQ=255)
                  tCACATATTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAg                                                                                                                          <  1:655419/141‑1 (MQ=255)
                      atatTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTACATAAACTTGCTTTCTATTCAATTGCCAAAGTTGAATAAAATTACATAAGtata                                                                                                                      >  1:330930/1‑141 (MQ=255)
                        atTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATaaa                                                                                                                    <  1:265266/141‑1 (MQ=255)
                               tactaTACAAGTATTAACAAACATCCCAACAAACCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAATTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCaat                                                                                                             >  2:665050/1‑141 (MQ=255)
                                gctaGACTAGTATTGACAAACAGCACAACAATCCCAAAACGTGCATGTGCTAACTTATGAATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATGGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCtata                                                                                                            <  2:742321/140‑1 (MQ=255)
                                 ctaTACAAGTATTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCaataa                                                                                                           >  1:250172/1‑141 (MQ=255)
                                      cAAGTATGAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAAt                                                                                                      <  1:441735/141‑1 (MQ=255)
                                        aGTATTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATaa                                                                                                    >  2:720487/1‑140 (MQ=255)
                                           aTTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGt                                                                                                 >  2:409862/1‑141 (MQ=255)
                                            ttAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGtt                                                                                                <  2:21203/141‑1 (MQ=255)
                                             tAACAAACATCCCAACAATCCCAAAACTTGTATGTGATAACTTATGCATAAAACTACAATTGTAAATAAAATAGCTTTATATTCAAAAATCAAAGTTGAATAAAATTAAATAACTATAAAAACCAAAAATCAAttgcataa                                                                                               >  2:193915/1‑134 (MQ=255)
                                              aacaaacaTGCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGGGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCTATAATGAATAGAGTTaa                                                                                              >  1:231147/1‑141 (MQ=255)
                                              aacaaacaTCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTaa                                                                                              >  2:126307/1‑141 (MQ=255)
                                               acaaacaTCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAATGTTGAATAAAATTAAATAAGTATAAAAACCAATACTCAATAGAGTTAat                                                                                             >  1:340436/1‑141 (MQ=255)
                                               acaaacaTCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAat                                                                                             <  1:76877/141‑1 (MQ=255)
                                                  aacaTGCCAAAAATCCGGAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAATGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATAtt                                                                                          <  2:65912/141‑1 (MQ=255)
                                                  aacaTCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATATAGTTAATAtt                                                                                          >  2:374847/1‑141 (MQ=255)
                                                    caTCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTa                                                                                        <  1:457341/141‑1 (MQ=255)
                                                       cccAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGaa                                                                                     >  2:306141/1‑141 (MQ=255)
                                                       cccAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGATGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGaa                                                                                     >  2:702273/1‑141 (MQ=255)
                                                           acaaTCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTAAATTGTCAAAATTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATaa                                                                                 <  2:597460/141‑1 (MQ=255)
                                                             aaTCCCAAAACTTGTATGTGCTAACTTATGCGTAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGa                                                                               <  1:74681/141‑1 (MQ=255)
                                                                      aCTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTAc                                                                      >  1:338993/1‑141 (MQ=255)
                                                                          gTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATaa                                                                  >  1:339027/1‑141 (MQ=255)
                                                                           tATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTAAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACAAATAATCAATAGAATTAATATTTAGAAATAAAATAATAGTACATaaa                                                                 >  2:205956/1‑141 (MQ=255)
                                                                             tgtgCTAACTTATGAATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAAc                                                               <  2:147040/141‑1 (MQ=255)
                                                                                 cTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAACAAAt                                                           <  2:69705/141‑1 (MQ=255)
                                                                                      ttATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAACAAATCActc                                                      <  2:250172/141‑1 (MQ=255)
                                                                                           cATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACAGAAAACAAATCACTCTATTa                                                 >  1:422401/1‑141 (MQ=255)
                                                                                               aaaCTACAAGTGTCAATAAACTTGCTTCCTATTCAATTGTCCAAGTTGCATAAAATTAAATAAGTATAAAAACCACTAATCAATCACCTTAATATTTAGAAATAAGATAATAGTACATAACACAACTCACTCTAttccctc                                             >  2:304720/1‑136 (MQ=255)
                                                                                                       aGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAACAAATCACTCTATTACATATTAAtttt                                     <  1:373099/141‑1 (MQ=255)
                                                                                                           taaataaaCTTGCTTTCTATTCAATTGTCAAGGTTAAGTAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAACAAATCACTCTATTACATATTAATTTTATaa                                 >  2:615777/1‑141 (MQ=255)
                                                                                                           taaataaaCTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAACAAATCACTCTATTACATATTAATTTTATaa                                 >  2:638472/1‑141 (MQ=255)
                                                                                                             aataaaCTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAACAAATCACTCTATTACATATTAATTTTATAAtt                               >  2:615594/1‑141 (MQ=255)
                                                                                                              ataaaCTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAACAAATCACTCTATTACATATTAATTTTATAAttt                              >  1:667468/1‑141 (MQ=255)
                                                                                                               taaaCTTGCTTTCTATTCAATTGTCAATGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAACAAATCACTCTATTACATATTAATTTTATAATTta                             >  1:186958/1‑141 (MQ=255)
                                                                                                                 aaCTTGCTTTCTATTCAATTGTCAAAGATGAAGAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAACAAATCACTCTATTACATATTAATTTTATAATTtata                           >  2:92483/1‑141 (MQ=255)
                                                                                                                        tttCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAACAAATCACTCTATTACATATTAATTTTATAATTTATATACAAAg                    <  1:409862/141‑1 (MQ=255)
                                                                                                                         ttCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAGGGTCATTAAAAGGACATAAAACAAATCACTCTATTACATATTAATTTTATAATTTATATACAAAGa                   >  1:175471/1‑141 (MQ=255)
                                                                                                                         ttCTATACAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCATTCCGCAATGCAAGCAAGCTCAAGCCCATACAGAATAGTACATAAAACAAATCACTCTATTACATATTAATTTTATAATTTATATACAAAGa                   <  2:733396/141‑1 (MQ=255)
                                                                                                                          tCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAACAAATCACTCTATTACATATTAATTTTATAATTTATATACAAAGaa                  >  1:556263/1‑141 (MQ=255)
                                                                                                                               tCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAACAAATCACTCTATTACATATTAATTTTATAATTTATATACAAAGAAAatat             <  1:156383/141‑1 (MQ=255)
                                                                                                                                cAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAACAAATCACTCTATTACATATTAATTATATAGTTTACAATTATAGAAAatata            >  1:743399/1‑141 (MQ=255)
                                                                                                                                      tCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAACAAATCACTCTATTACATATTAATTTTATAATTTATATACAAAGAAAATATATCAata      >  2:267223/1‑141 (MQ=255)
                                                                                                                                         aaGTTGAATAAAATTAAATAAGTATAAAAAACCATAAAAAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAACAAATCACTCTATTACATATTAATTTTCTAATTTATATACAAAAAAAATATATAAATATTa   >  2:53247/1‑141 (MQ=255)
                                                                                                                                          aGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAACAAATCACTCTATTACATATTAATTTTATAATTTATATACAAAGAAATTATATCAATATTAc  >  2:151959/1‑141 (MQ=255)
                                                                                                                                          |                                                                                                                                            
ACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAACTTGCTTTCTATTCAATTGTCAAAGTTGAATAAAATTAAATAAGTATAAAAACCAATAATCAATAGAGTTAATATTTAGAAATAAGATAATAGTACATAAAACAAATCACTCTATTACATATTAATTTTATAATTTATATACAAAGAAAATATATCAATATTAC  >  USA300TCH1516_ALE/1891913‑1892191

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: ‑