Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 870,161 G→T 12.9% intergenic (‑37/+155) USA300HOU_0814 ← / ← USA300HOU_0815 hypothetical protein/hypothetical lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730870,1610GT12.9% 105.8 / 2.1 41intergenic (‑37/+155)USA300HOU_0814/USA300HOU_0815hypothetical protein/hypothetical lipoprotein
Reads supporting (aligned to +/- strand):  ref base G (14/21);  new base T (4/2);  total (18/23)
Fisher's exact test for biased strand distribution p-value = 3.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGTAGAATCTTTAATACCAGTTCCCATCAATGCTTGTGAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAGTTTCTCTAAAAATTAAATAACTGAATGTAA  >  CP000730/870028‑870296
                                                                                                                                     |                                                                                                                                       
cAGTAGAATCTTTAATACCAGTTCCCATCAATGCTTGTGAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGCTTTTcc                                                                                                                                  >  2:373063/1‑141 (MQ=255)
         cTTTAATACCAGTTCCCATCAATGCTTGTGAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACgggg                                                                                                                         <  2:101772/141‑1 (MQ=255)
          tttAATACCAGTTCCCATCAATGCTTGTGAAACTTGACCTTGTTCATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGa                                                                                                                        <  2:365798/141‑1 (MQ=255)
             aaTACCAGTTCCCATCAATGCTTGTGAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTg                                                                                                                     <  1:286943/141‑1 (MQ=255)
              aTACCGGTTCCCATCAATGCTTGTGAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGa                                                                                                                    <  2:56996/141‑1 (MQ=255)
              aTACCAGTTCCCATCAATGCTTGTTAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGa                                                                                                                    <  2:147408/141‑1 (MQ=255)
                 ccAGTTCCCATCAATGCTTGTGAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTTTTTTTTTCTGGCACGGGGACTGAttt                                                                                                                 >  2:261236/1‑141 (MQ=255)
                  cggTTCCCATCAATCCTTTTGAATCTTTACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTc                                                                                                                <  2:338498/139‑1 (MQ=255)
                          aTCAATGCTTGTGAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAacac                                                                                                        >  1:116077/1‑141 (MQ=255)
                                   tgttAAACTTTACCTTGTACGTTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAaca                                                                                               <  2:242030/141‑1 (MQ=255)
                                   tgtgAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGGCTGATTTCTTTACCACCATTAAaca                                                                                               >  1:108013/1‑141 (MQ=255)
                                     tgAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAAcaca                                                                                             <  1:238749/141‑1 (MQ=255)
                                         aCTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGCtt                                                                                         >  1:194450/1‑141 (MQ=255)
                                         aCTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGAtt                                                                                         >  2:225152/1‑141 (MQ=255)
                                               ccTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTTTTTTTTTTTTGTTCGTGGCCTCTTTTCTTTTCCTCCATTTAAGACAGCTtttttat                                                                                   >  2:303391/1‑141 (MQ=255)
                                                 ttGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATtttttattt                                                                                 <  1:212689/141‑1 (MQ=255)
                                                         ttCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTCTTTATTTTTAATCAt                                                                         <  1:186515/141‑1 (MQ=255)
                                                         ttCCACATTTAGCCTCTTCTTATTTTAATGCATTATTCAATGCGGGATTTACAAATTAATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCAt                                                                         <  1:5268/141‑1 (MQ=255)
                                                          tCCCCATGTAGCCTCTTCTTGTTTTAATGCATAATTCAATGCGGGATTTACAAATTTATCCCGTCTTTTTTTTGTGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATa                                                                        >  1:267748/1‑141 (MQ=255)
                                                              cATGTGGCCTCTTCTTGTTTTAATGCAGTATGCAATGCGGTATTTAAAGATTTATCACATCTTTTTTTTATTATTTTCACGCGGGTGCACGTTGGTCTTCAAAAGAGTTAAAGACAGATTTTTTATGTTTAAACATAGCtt                                                                    <  2:78718/141‑1 (MQ=255)
                                                                     ccTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTa                                                             <  1:151789/141‑1 (MQ=255)
                                                                     ccTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCAGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATCGTa                                                             >  2:26926/1‑141 (MQ=255)
                                                                      ctctTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTTTGATTTTTCGGCACGGGGACTGAATTCTTTAACACCTTTAAACACTGATTTTTTATTTTTAATCATAGCTTTTTCGTAt                                                            >  2:46227/1‑141 (MQ=255)
                                                                      ctctTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTAt                                                            <  2:61202/141‑1 (MQ=255)
                                                                           cttGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGt                                                       <  2:365144/141‑1 (MQ=255)
                                                                               ttttAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTGAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGc                                                   <  1:331077/141‑1 (MQ=255)
                                                                                        attattCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTTTTTTTTTCCAGCACGGGGACGGATTTCTTTAACACCTTTGGACACGGAGTTTTTATTTGTGATCTTAGCTTTTTATTATCATGTTTGTTAAGCtatg                                          >  2:362528/1‑140 (MQ=255)
                                                                                        attattCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCtata                                          >  1:300923/1‑141 (MQ=255)
                                                                                            ttCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCAAGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTttaaata                                      >  2:118992/1‑141 (MQ=255)
                                                                                                aTGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGTGTTCTTATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTc                                  <  2:248976/141‑1 (MQ=255)
                                                                                                 tGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGtaa                                 >  1:218268/1‑139 (MQ=255)
                                                                                                  gCGGGATTTCCAAATTTCTCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAg                                <  1:66111/141‑1 (MQ=255)
                                                                                                   cGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACCCCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTCGCTAAGCTATAAATAAGTCAGt                               >  2:50587/1‑141 (MQ=255)
                                                                                                   cGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAGt                               <  2:15473/141‑1 (MQ=255)
                                                                                                      gATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAGTTtc                            >  2:220687/1‑141 (MQ=255)
                                                                                                            cAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAGTTTCTCTaaa                      >  1:211952/1‑141 (MQ=255)
                                                                                                                         tCTTTTTTTTATTATTTCCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAGTTTCTCTAAAAATTAAATAACTg         <  1:46227/141‑1 (MQ=255)
                                                                                                                         tCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAGTTTCTCTAAAAATTAAATAACTg         <  1:338205/141‑1 (MQ=255)
                                                                                                                          cTTTTTTTTTTTTTTTTCCGGCACGGGGACTGATTTCTTTAACACCCTTATACACAGATTTTTTATTTTTAATCATCGCTTCTTAGTATCCTGTTGGCTTATCTTTAAATCATTCAGTTTCTCTCAAAATTAAATCAcccc        >  2:36941/1‑138 (MQ=255)
                                                                                                                              tttttATGATTTTCCGGCATGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAGTTTCTCTAAAAATTAAATAACTGAATGt    <  1:238059/141‑1 (MQ=255)
                                                                                                                                tttATGATTTTCCGGCACGGGGACTGATTTCTTTTTCACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAGTTTCTCTAAAAATTAAATAACTGAATGTaa  <  1:348566/141‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                       
CAGTAGAATCTTTAATACCAGTTCCCATCAATGCTTGTGAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAGTTTCTCTAAAAATTAAATAACTGAATGTAA  >  CP000730/870028‑870296

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: ‑