Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,642,644 T→A 10.6% intergenic (‑2/+65) ydaT ← / ← USA300HOU_2498 hypothetical protein/hypothetical membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,642,6440TA10.6% 104.8 / 4.4 41intergenic (‑2/+65)ydaT/USA300HOU_2498hypothetical protein/hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base T (19/16);  new base A (2/2);  total (23/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.10e-01

TAATTACTTCAAATTCTTTCCATTTTTCGGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTCACGAAAACCATTGTGTTGAATATTCATCATTGCTGATTGAATATAAT  >  CP000730/2642516‑2642776
                                                                                                                                |                                                                                                                                    
tAATTACTTCAAATTCTTTCCATTTTTCGGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTc                                                                                                                          <  1:12851/141‑1 (MQ=255)
 aaTTACTTCAAATTCTTTCCATTTTTCGGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTcc                                                                                                                         <  1:444750/141‑1 (MQ=255)
       ttCAAATTCTTTCCATTTTTCGGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCATCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCat                                                                                                                   <  1:348437/141‑1 (MQ=255)
              tCTTTCCATTTTTCGGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACt                                                                                                            >  2:17936/1‑141 (MQ=255)
               cTTTCCATTTTTTTTGTTTATTTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATGTGTTAGAATTCAAGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTATTCTCCCGTCATAATAACtt                                                                                                           >  2:194854/1‑141 (MQ=255)
                tttCCATTTTTCGGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTc                                                                                                          >  1:395779/1‑141 (MQ=255)
                   ccATTTTTCGGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGa                                                                                                       <  1:424362/141‑1 (MQ=255)
                   ccATTTTTCGGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGa                                                                                                       <  2:443844/141‑1 (MQ=255)
                         ttCGGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACg                                                                                                 >  2:55707/1‑141 (MQ=255)
                                       tCATTGTAAAGGGCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGa                                                                                   <  1:335903/141‑1 (MQ=255)
                                       tCATTGTAAAGGGCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGa                                                                                   <  1:335966/141‑1 (MQ=255)
                                        cATTGTAAAGGGCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACAATTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGAt                                                                                  >  2:95049/1‑141 (MQ=255)
                                        cATTGTAAAGGGCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACAATTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGAt                                                                                  >  2:165387/1‑141 (MQ=255)
                                          aatgaaaGGGCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATaa                                                                                >  2:390326/5‑141 (MQ=255)
                                              aaaGGGCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAatat                                                                            >  2:337780/1‑141 (MQ=255)
                                                 gggCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTa                                                                         <  1:408194/141‑1 (MQ=255)
                                                  ggCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTaa                                                                        >  1:428929/1‑141 (MQ=255)
                                                   gtagttCCTCAACCTCCAATATGTTATAATTACTGTTATATACCACCATAATTATAAAATGAAACATATTAATCACATTTTTTGATACTCCCGTCATAATAACTTCTGACAAACGTTAGTCAAACCTGATAACTATTTaaa                                                                       <  2:122749/137‑2 (MQ=255)
                                                    cATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAAtt                                                                      >  2:107977/1‑141 (MQ=255)
                                                    cATTTACTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACAATTTTTTAGCCTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTTAtt                                                                      <  2:273535/141‑1 (MQ=255)
                                                      tttCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAAtttt                                                                    >  1:346408/1‑141 (MQ=255)
                                                      tttCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAAtttt                                                                    >  1:342380/1‑141 (MQ=255)
                                                      tttCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCGGATAAATATTTAAtttt                                                                    >  1:3567/1‑141 (MQ=255)
                                                            tAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGt                                                              <  2:356989/141‑1 (MQ=255)
                                                             aaCCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTACTTTTAAACGtt                                                             >  2:424031/1‑141 (MQ=255)
                                                             aaCCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGtt                                                             >  2:77201/1‑141 (MQ=255)
                                                                       atGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACAATTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTTATTTTAAACGTTCTTGtctctc                                                   <  2:379083/141‑1 (MQ=255)
                                                                        tGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGtctctct                                                  >  2:24381/1‑141 (MQ=255)
                                                                         gTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGtctctctc                                                 <  2:81233/141‑1 (MQ=255)
                                                                          ttATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTCa                                                >  1:66982/1‑141 (MQ=255)
                                                                          ttATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTCa                                                >  1:67048/1‑141 (MQ=255)
                                                                           tataATTCATGTTATATACCACAATAATTATAAAATGAAACATATTAAACACATTGTTTTAAACTCCCGACATAATAACTTCAGGCGAACGATGGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTCAc                                               >  1:130342/1‑141 (MQ=255)
                                                                                    tGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTCACGAAAACCAt                                      >  1:337384/1‑141 (MQ=255)
                                                                                    tGTTATATACCACCATAAGTATAAAAGGAAACATAATAAACTCACTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGTCCTGATAAATATATAATTTTAAACGTTCTTGTTTCTCTCACGaaatctat                                      >  2:104058/1‑136 (MQ=255)
                                                                                               accaTAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTCACGAAAACCATTGTGTTGAata                           >  1:387190/1‑141 (MQ=255)
                                                                                                  aTAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTCACGAAAACCATTGTGTTGAATATtc                        <  1:107969/141‑1 (MQ=255)
                                                                                                  aTAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTCACGAAAACCATTGTGTTGAATATtc                        <  1:118907/141‑1 (MQ=255)
                                                                                                              tGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTCACGAAAACCATTGTGTTGAATATTCATCATTGCTGAt            <  1:437770/141‑1 (MQ=255)
                                                                                                                 aaCATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTCACGAAAACCATTGTGTTGAATATTCATCATTGCTGATTGa         <  1:401493/141‑1 (MQ=255)
                                                                                                                   cATATTAAACACA‑TTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTCACGAAAACCATTGTGTTGAATATTCATCATTGCTGATTGAata      >  2:426072/1‑141 (MQ=255)
                                                                                                                        tAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTCACGAAAACCATTGTGTTGAATATTCATCATTGCTGATTGAATATAAt  <  1:55707/141‑1 (MQ=255)
                                                                                                                                tttttttAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTCACGAAAACCATTGTGTTg                               >  1:213263/1‑104 (MQ=255)
                                                                                                                                tttttttAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTCACGAAAACCATTGTGTTg                               <  2:213368/104‑1 (MQ=255)
                                                                                                                                tttttttAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTCACGAAAACCATTGTGTTg                               >  1:213368/1‑104 (MQ=255)
                                                                                                                                tttttttAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTCACGAAAACCATTGTGTTg                               <  2:213263/104‑1 (MQ=255)
                                                                                                                                |                                                                                                                                    
TAATTACTTCAAATTCTTTCCATTTTTCGGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTCACGAAAACCATTGTGTTGAATATTCATCATTGCTGATTGAATATAAT  >  CP000730/2642516‑2642776

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑