Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,596,868 A→T 9.7% Y212N (TAC→AAC)  nikA_2 ← Nickel‑binding periplasmic protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,596,8680AT 9.7% 123.8 / 4.5 41Y212N (TAC→AAC) nikA_2Nickel‑binding periplasmic protein
Reads supporting (aligned to +/- strand):  ref base A (16/21);  new base T (2/2);  total (18/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.76e-01

TGTCTAAGCTATCTGTACCTCTATCATCTGTGAAGGCAAAGTTCGTTTCACCTTTTTTCATTGATAGGAATGCTGTTTCACCAGCAGGCATTACTTTTGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTAAAGTCTTTTGGAGACACAAATACATATGGAC  >  USA300TCH1516_ALE/2596733‑2597008
                                                                                                                                       |                                                                                                                                            
tGTCTAAGCTATCTGTACCTCTATCATCTGTGAAGGCAAAGTTCGTTTCACCTTTTTTTTTTTTTTTGAATGCTGTTTCACCAGCAGGCATTACTTTTGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGAt                                                                                                                                         >  2:185492/1‑141 (MQ=255)
tGTCTAAGCTATCTATACCTCTATCATCTGTGAAGGCAAAGTTCGTTTCACCTTTTTTCTTTTTTATGAATGCTGTTTCACCAGCAGGCATTACTTTTGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGAt                                                                                                                                         >  2:66509/1‑141 (MQ=255)
     aaGCTATCTGTACCTCTATCATCTGTGAAGGCAAAGTTCGTTTCACCTTTTTTCATTGATAGGAATGCTGTTTCACCAGCAGGCATTACTTTTGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCAttt                                                                                                                                    >  2:240119/1‑141 (MQ=255)
              gTACCTCTATCATCTGTGAAGGCAAAGTTCGTTTCACCTTTTTTCATTGATAGGAATGCTGTTTCACCAGCAGGCATTACTTTTGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAg                                                                                                                           <  1:155397/141‑1 (MQ=255)
                 ccTCTATCATCTGTGAAGGCAAAGTTCGTTTCACCTTTTTTCATTGATAGGAATGCTGTTTCACCAGCAGGCATTACTTTTGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTTTTGATCATTTTTGTTAAAGTCt                                                                                                                        >  2:142061/1‑141 (MQ=255)
                 ccTCTATCATCTGTGAAGGCAAAGTTCGTTTCACCTTTTTTCATTGATAGGAATGCTGTTTCACCAGCAGGCATTACTTTTGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTTTTGATCATTTTTGTTAAAGTCt                                                                                                                        >  2:142083/1‑141 (MQ=255)
                        catcTGTGAAGGCAAAGTTCGTTTCACCTTTTTTCATTGATAGGAATGCTGTTTCACCAGCAGGCATTACTTTTGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACt                                                                                                                 <  2:192813/141‑1 (MQ=255)
                               gAAGGCAAAGTTCGTTTCACCTTTTTTCATTGATAGGAATGCTGTTTCACCAGCAGGCATTACTTTTGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCttt                                                                                                          <  2:192552/141‑1 (MQ=255)
                                    cAAAGTTCGTTTCACCTTTTTTCATTGATAGGAATGCTGTTTCACCAGCAGGCATTACTTTTGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTtgt                                                                                                     >  2:78873/1‑141 (MQ=255)
                                          tCGTTTCACCTTTTTTCATTGATAGGAATGCTGTTTCACCAGCAGGCATTACTTTTGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCAc                                                                                               >  1:93271/1‑141 (MQ=255)
                                                cACCTTTTTTCATTGATAGGAATGCTGTTTCACCAGCAGGCATTACTTTTGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAAtt                                                                                         <  2:92230/141‑1 (MQ=255)
                                                     tttttCATTGATAGGAATGCTGTTTCACCAGCAGGCATTACTTTTGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAAt                                                                                    <  2:199123/141‑1 (MQ=255)
                                                                    aaTGCTGTTTCACCAGCAGGCATTACTTTTGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCg                                                                     <  1:240119/141‑1 (MQ=255)
                                                                      tGCTGTTTCACCAGCAGGCATTACTTTTGCTTGTACTTTGTTAAGTTTAGCCTTTTCGCCCCCGTATTGATCATTTTTGTTAACGTCTGCAGACTCATCTTTTTTGTGTTCACCCACTTTAAATGGACCAGTACCATCGaa                                                                   <  2:55275/141‑1 (MQ=255)
                                                                            ttCACCAGCAGGCATTACTTTTGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACttttt                                                             >  1:164130/1‑141 (MQ=255)
                                                                                   gcagGCATTACTTTTGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCa                                                      >  1:182376/1‑141 (MQ=255)
                                                                                              ttttGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTtgttgt                                           >  1:21347/1‑141 (MQ=255)
                                                                                                 tGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTAcc                                        <  1:66509/141‑1 (MQ=255)
                                                                                                 tGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTAcc                                        >  1:110922/1‑141 (MQ=255)
                                                                                                 tGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTAcc                                        >  1:110885/1‑141 (MQ=255)
                                                                                                 tGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTAcc                                        <  1:229394/141‑1 (MQ=255)
                                                                                                 tGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTAcc                                        <  1:185492/141‑1 (MQ=255)
                                                                                                    ttGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGtt                                     >  1:63016/1‑141 (MQ=255)
                                                                                                    ttGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGtt                                     <  1:156563/141‑1 (MQ=255)
                                                                                                    ttGTACTTTGTTAAGTTTAGACTTTGCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGtt                                     >  2:187795/1‑141 (MQ=255)
                                                                                                        aCTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTa                                 <  2:65951/141‑1 (MQ=255)
                                                                                                         cTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTaa                                >  1:204505/1‑141 (MQ=255)
                                                                                                           ttGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTAAAg                              <  2:61633/141‑1 (MQ=255)
                                                                                                             gTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTAAAGTc                            >  1:15826/1‑141 (MQ=255)
                                                                                                             gTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTAAAGTc                            >  1:163719/1‑141 (MQ=255)
                                                                                                             gTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTAAAGTc                            <  1:23515/141‑1 (MQ=255)
                                                                                                             gTTAAGTTTAGACTTTCCGGATCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTAAAGTc                            <  1:2273/141‑1 (MQ=255)
                                                                                                              ttAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTAAAGTCt                           <  1:171316/141‑1 (MQ=255)
                                                                                                                 aGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTAAAGTCtttt                        <  2:144332/141‑1 (MQ=255)
                                                                                                                  gTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTAAAGTCTTTTg                       >  2:220816/1‑141 (MQ=255)
                                                                                                                   tttAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTAAAGTCTTTTgg                      <  2:93271/141‑1 (MQ=255)
                                                                                                                        aCTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTAAAGTCTTTTGGAGaca                 <  2:217934/141‑1 (MQ=255)
                                                                                                                          ttttCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTAAAGTCTTTTGGAGacacc               <  1:248010/141‑2 (MQ=255)
                                                                                                                          ttttCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTAAAGTCTTTTGGAGAcaca               <  1:116010/141‑1 (MQ=255)
                                                                                                                                ccccAGTTTTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTAAAGTCTTTTGGAGACACAAATACa         <  1:142083/141‑1 (MQ=255)
                                                                                                                                ccccAGTTTTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTAAAGTCTTTTGGAGACACAAATACa         <  1:142061/141‑1 (MQ=255)
                                                                                                                                       aTTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTAAAGTCTTTTGGAGACACAAATACATATGGAc  <  2:21347/141‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                            
TGTCTAAGCTATCTGTACCTCTATCATCTGTGAAGGCAAAGTTCGTTTCACCTTTTTTCATTGATAGGAATGCTGTTTCACCAGCAGGCATTACTTTTGCTTGTACTTTGTTAAGTTTAGACTTTTCGCCCCAGTATTGATCATTTTTGTTAAAGTCTGCAGACTCATCTTTTTTGTGTTCACCTAATTTAAATGGACCAGTACCATCGAACTTTTTAACGCCATCTTTTGTTGTACCGTTTTTAAAGTCTTTTGGAGACACAAATACATATGGAC  >  USA300TCH1516_ALE/2596733‑2597008

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