Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,466,928 T→C 12.5% F18S (TTC→TCC)  USA300HOU_2329 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,466,9280TC12.5% 89.0 / 2.2 38F18S (TTC→TCC) USA300HOU_2329hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (17/16);  new base C (3/2);  total (20/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTAAATAACGAATTCTCTATTATTTTATCATGAATTAAATAACGTGTATGTCTTAATTTATTTTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGTGAATCGTTTTAATTACAGCCACGGTCTTTCTTTAAAAGAACGCGAAAATTTAGCATATACGCTATTTACACTAGAAGAA  >  CP000730/2466791‑2467067
                                                                                                                                         |                                                                                                                                           
cTAAATAACGAATTCTCTATTATTTTATCATGAATTAAATAACGTGTATGTCTTAATTTATTTTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAGACCGTAACATCTGAATTCAt                                                                                                                                          <  2:181704/141‑1 (MQ=255)
 tAAATAACGAATTCTCTATTATTTTATCATGAATTAAATAACGTGTATGTCTTAATTTATTTTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACACAAACCGTAACATCTGAATCCAtt                                                                                                                                         >  2:141903/1‑141 (MQ=255)
    aTAACGAATTCTCTATTATTTTATCATGAATTAAATAACGTGTATGTCTTAATTTATTTTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAGTTCATTGAc                                                                                                                                      <  2:270604/141‑1 (MQ=255)
    aTAACGAATTCTCTATTATTTTATCATGAATTAAATAACGTGTATGTCTTAATTTATTTTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATCCATTGAc                                                                                                                                      >  2:304827/1‑141 (MQ=255)
    aTAACGAATTCTCTATTATTTTATCATGAATTAAATAACGTGTATGTCTTAATTTATTTTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATCCATTGAc                                                                                                                                      >  2:128670/1‑141 (MQ=255)
         gAATTCTCTATTATTTTATCATGAATTAAATAACGTGTATGTCTTAATTTATTTTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATaa                                                                                                                                 <  1:183589/141‑1 (MQ=255)
          tattggttgttattTCATCATGAATTAAATAACGTGTATGGCTTAATTTATTTTAGTATGATAGTCACTAAGGATATGGTTATTATCAAACAACTTTTCACACATACTCAAACCGTAACATCTGAACTCATTGACCATAAc                                                                                                                                <  2:275319/132‑1 (MQ=255)
           aTTCTCTATTATTTTATGATGAATTAAATAACGTGTATGTCTTAATTTATTTTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACa                                                                                                                               <  2:40650/141‑1 (MQ=255)
             tctcTATTATTTTATCATGAATTAAATAACGTGTATGTCTTAATTTATTTTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATCCCCAAACCGTAACATCTGAATTCATTGACCTTAACAAt                                                                                                                             <  2:19213/141‑1 (MQ=255)
                     attTTATCATGAATTAAATAACGTGTATGTCTTAATTTATTTTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCAAATGCa                                                                                                                     >  2:38787/1‑141 (MQ=255)
                      ttttATCATGAATTAAATAACGTGTATGTCTTAATTTATTTTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCat                                                                                                                    <  1:29789/141‑1 (MQ=255)
                        ttATCATGAATTAAATAACGTGTATGTCTTAATTTATTTTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCatga                                                                                                                  >  1:119220/1‑141 (MQ=255)
                          aTCATGAATTAAATAACGTGTATGTCTTAATTTATTTTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCatgatg                                                                                                                >  2:237527/1‑141 (MQ=255)
                           tCATTAATTAAATAACGTGTATGTCTTAATTTATTTTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGc                                                                                                               <  2:324573/141‑1 (MQ=255)
                           tCAGGAATTAAATAACGTGTATGTTTTAATTTATTTTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGc                                                                                                               <  2:117511/141‑1 (MQ=255)
                               gcaTTAAATAACGTGTATGTCTTAATGTATTTTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTGTTTACACATACTCAAACCGTAACATGTGAATTCAATGACCATAACAATCATATGCATGATCCAAAt                                                                                                           <  1:245048/139‑1 (MQ=255)
                                        aaCGTGTATGTCTTAATTTATTCTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATc                                                                                                  <  1:190483/141‑1 (MQ=255)
                                                        tttatttTAGTAGGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGAcgtcg                                                                                  <  2:131764/141‑1 (MQ=255)
                                                         ttatttTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGAcgtcgt                                                                                 <  1:134609/141‑1 (MQ=255)
                                                         ttatttTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGAcgtcgt                                                                                 <  1:278500/141‑1 (MQ=255)
                                                                      aTAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGTGAATCGTTTTAAt                                                                    >  2:166551/1‑141 (MQ=255)
                                                                      aTAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGGGAATCGTTTTAAt                                                                    >  1:266502/1‑141 (MQ=255)
                                                                       tAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGTGAATCGTTTTAAtt                                                                   >  1:3285/1‑141 (MQ=255)
                                                                        aGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGTGAATCGTTTTAATTa                                                                  >  1:163539/1‑141 (MQ=255)
                                                                        aGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGTGAATCGTTTTAATTa                                                                  <  1:27316/141‑1 (MQ=255)
                                                                           cACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGTGAATCGTTTTATTTACac                                                               >  2:209807/1‑140 (MQ=255)
                                                                             cTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGTGAAACGTATTAATTACAGcc                                                             >  1:201086/1‑141 (MQ=255)
                                                                                 ggAGATGGTTATTAACAAAAAACTTGTTACACATACTCAAACCGGAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGTGAATCGTTTTAATTACAGCCACgg                                                         >  1:182188/1‑141 (MQ=255)
                                                                                   agaTGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGTGAATCGTTTTAATTACAGCCACGGtc                                                       >  1:41869/1‑141 (MQ=255)
                                                                                         ttattaTCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGTGAATCGTTTTAATTACAGCCACGGtctttctt                                                 >  2:253247/1‑141 (MQ=255)
                                                                                                 aaaCAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGTGAATCGTTTTAATTACAGCCACGGTCTTTCTTTACAAGaa                                         >  1:129932/1‑141 (MQ=255)
                                                                                                         ttttACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGTGAATCGTTTTAATTACAGCCACGGTCTTTCTTTAAAAGAACGCGaaaa                                 >  2:261579/1‑141 (MQ=255)
                                                                                                           ttACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGAAGTGAATCGTTTTAATTACAGAAAAGGTATGCTTCGAAAAGAACGCGAAAAtt                               >  2:149598/1‑141 (MQ=255)
                                                                                                               acaTACTCAAACCGTAACATCTGAATCCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGTGAATCGTTTTAATTACAGCCACGGTCTTTCTTTAAAAGAACGCGAAAATTTAGc                           <  1:304827/141‑1 (MQ=255)
                                                                                                               acaTACTCAAACCGTAACATCTGAATCCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGTGAATCGTTTTAATTACAGCCACGGTCTTTCTTTAAAAGAACGCGAAAATTTAGc                           <  1:128670/141‑1 (MQ=255)
                                                                                                                        aaCCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGTGAATCGTTTTAATTACAGCCACGGTCTTTCTTTAAAAGAACGCGAAAATTTAGCATATACGCt                  >  1:32698/1‑141 (MQ=255)
                                                                                                                                cATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGTGAATCGTTTTAATTACAGCCACGGTCTTTCTTTAAAAGAACACGAAAATTTAGCATATACGCTATTTaccc          >  1:178054/1‑139 (MQ=255)
                                                                                                                                   cTGAATTCATGTACCATAACAATCATATGCTTTATGCAAATGATAAGATCATTTTTAGTGACGTCGTGAATCGTTTTAATTACAGCCACGGTCTTTCTTTAAAAGAACGCGAAAATTTAGCATATACGCTATTTACACTag       <  1:149598/141‑1 (MQ=255)
                                                                                                                                        ttCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGTGAATCGTTTTAATTACAGCCACGGTCTTTCTTTAAAAGAACGCGAAAATTTAGCATATACGCTATTTACACTAgaagaa  <  2:293120/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                           
CTAAATAACGAATTCTCTATTATTTTATCATGAATTAAATAACGTGTATGTCTTAATTTATTTTAGTATGATAGTCACTAAGGAGATGGTTATTATCAAACAACTTTTTACACATACTCAAACCGTAACATCTGAATTCATTGACCATAACAATCATATGCATGATGCAAATTATAATATCATTTTTAGTGACGTCGTGAATCGTTTTAATTACAGCCACGGTCTTTCTTTAAAAGAACGCGAAAATTTAGCATATACGCTATTTACACTAGAAGAA  >  CP000730/2466791‑2467067

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑