Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,149,822 G→T 11.1% G68C (GGT→TGT)  agrA → Accessory gene regulator A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,149,8220GT11.1% 134.9 / 2.5 54G68C (GGT→TGT) agrAAccessory gene regulator A
Reads supporting (aligned to +/- strand):  ref base G (29/18);  new base T (3/4);  total (32/22)
Fisher's exact test for biased strand distribution p-value = 4.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AATGATAGAAGAAAAGCCTATGGAAATTGCCCTCGCAACTGATAATCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGTCACAGTGAACTTACCTATTTAACATTTGTCTACAAAGTTGCAGCGATGGATTTTATTTTTAAAGAT  >  USA300TCH1516_ALE/2149692‑2149953
                                                                                                                                  |                                                                                                                                   
aaTTATATAAGTAAAGCCTATGGAAATTGCCCTCGCAACTGATAATCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTa                                                                                                                                  <  1:59832/134‑1 (MQ=255)
aaTGATAGAAGAAAAGCCTATGGAAATTGCCCTCGCAACTGATAATCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTa                                                                                                                                  <  1:391688/134‑1 (MQ=255)
         agaaAAGCCTATGGAAATTGCCCTCGCAACTGATAATCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATTGTATCAAATTAg                                                                                                                         >  2:388499/1‑134 (MQ=255)
         agaaAAGCCTATGGAAATTGCCCTCGCAACTGATAATCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTGTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAg                                                                                                                         >  2:313113/1‑134 (MQ=255)
            aaaGCCTATGGAAATTGCCCTCGCAACTGATAATCCTTATGCGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCa                                                                                                                      >  1:1822/1‑134 (MQ=255)
              aGCCTATGGAAATTGCCCTCGCAACTGATAATCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACAGATATTAATGATATCAAATTAGGCAGt                                                                                                                    >  1:150884/1‑134 (MQ=255)
                ccTATGGAAATTGCACTCGCAACTGATAATCCTTATGAGGTGCGGTAGCAAGCAAGAGATATGCATGACATAGGCTGTTACGTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCACTGa                                                                                                                  >  2:165766/1‑134 (MQ=255)
                     ggAAATTGCCCTGGCAAATGATACCCCTTATTAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTATATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTc                                                                                                             <  2:554895/134‑1 (MQ=255)
                      gAAATTGCCCTCGCAACTGATAATCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATTTTTTTTGTCTCAAATTATTCAGTGAAATTCg                                                                                                            <  2:497655/134‑1 (MQ=255)
                      gAAATTGCCCTCGCAACTGATAATCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCg                                                                                                            >  1:291765/1‑134 (MQ=255)
                        aaTTGCCCTCGCAACTGATAATCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCATa                                                                                                          >  1:288626/1‑134 (MQ=255)
                         aTTGCCCTCGCAACTGATAATCCTTAGGAGGTGCATAGGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTaa                                                                                                         <  2:427250/134‑1 (MQ=255)
                             ccatCGCAACTGATAATCCTTATGAGGTGATTGAGCAAGCTAAAAATGTGAATGACATAGGGTGTTACTTTTTAGATTTACAATTTTTAACTAACATTATTGGAAGCAAAGTATACATAGAAATTTGTCAGCAt                                                                                                     >  2:228047/4‑134 (MQ=255)
                             cacTCGCAACTGATAATCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACAGAGGCTGTTACTGGTTAGATATTCAACTTTCAACTGATATTAATGATATCAAATTAGTCAGTGAAATTCGTAAgaaa                                                                                                     >  2:295528/3‑131 (MQ=255)
                              ccTCGCAACTGATAATCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCTACTGATATTAATGGTATCCAATTAGGCAGTGAAATTCGTAAACATg                                                                                                    >  1:113162/1‑134 (MQ=255)
                              ccTCGCAACTGATAATCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATg                                                                                                    <  2:188743/134‑1 (MQ=255)
                                      cTGATAATCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGTTGTTATTTTTTAGATTTTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGtt                                                                                            <  1:26141/134‑1 (MQ=255)
                                      cTGATAATCATTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGtt                                                                                            <  1:607161/134‑1 (MQ=255)
                                         aTAATCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGt                                                                                         <  1:488050/134‑1 (MQ=255)
                                         aTAATCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGt                                                                                         >  2:313179/1‑134 (MQ=255)
                                         aTAATCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGt                                                                                         <  2:310723/134‑1 (MQ=255)
                                            aTCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAAc                                                                                      >  1:160472/1‑134 (MQ=255)
                                                ttATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATTGTATCAAATTAAGCAGTAAAAGTCGTAAGCATGACTCAGTTGGTAACatta                                                                                  >  2:124637/1‑134 (MQ=255)
                                                      ggTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCg                                                                            <  2:444382/134‑1 (MQ=255)
                                                      ggTGCTTGAGCAAACTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCg                                                                            <  2:559841/134‑1 (MQ=255)
                                                        tGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGtt                                                                          <  2:517138/134‑1 (MQ=255)
                                                          cTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATTGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTAc                                                                        <  1:406838/134‑1 (MQ=255)
                                                           ttGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACg                                                                       >  1:403092/1‑134 (MQ=255)
                                                              aGCAAGCTAATATTTTGAATATCATAGGCTGTTACTTTGTAGATATTGTCCTGTCAACTGATATTGATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGt                                                                    <  1:414508/134‑1 (MQ=255)
                                                               gCAAGATAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGTc                                                                   <  2:558393/134‑1 (MQ=255)
                                                                             tgaatgaCATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGTCACAGTGAACTTAcc                                                     <  2:291765/134‑1 (MQ=255)
                                                                              gaatgaCATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCTTGACCCAGCTAGAAAAATTATTTTCGATACAAGTCACAGTGAACTTACCt                                                    >  1:539562/1‑134 (MQ=255)
                                                                               aatgaCATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGCTATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTGGGTAACATTCTTTTCGTTACGAGTCACAGTTAAATTCCCTa                                                   >  1:153957/1‑134 (MQ=255)
                                                                                 tgaCATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCCGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGACACAGCGAACATACCTAtt                                                 >  1:162730/1‑134 (MQ=255)
                                                                                 tgaCATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGCCCCAGTTGGTCACATTATTCTCGTTTCGAGTCACAGTGCACCTACCTGtt                                                 >  1:219479/1‑134 (MQ=255)
                                                                                 tgaCATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGTCACAGTGAACTTACCTAtt                                                 >  1:593855/1‑134 (MQ=255)
                                                                                 tgaCATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGTCACAGTGAAATTACCTAtt                                                 >  1:324964/1‑134 (MQ=255)
                                                                                        ggCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGTCACAGTGAACTTACCTATTTAACAtt                                          >  1:298034/1‑134 (MQ=255)
                                                                                         gCTGTTACTTTTTAGATATTCAAGTTTCAACTGATATTAATGGTATGAAATTAGGCAGTAAAATTCGTAAGCATGACACAGTTGGTACCATTAGTTGCGTCACGAAAAAAAATGAACTTACCAATTGAACaaac                                         >  2:151191/1‑131 (MQ=255)
                                                                                            gTTACTTTTTAGATATTCAACTTTCAACTGATATTAATTGTATCACATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGTCACAGTGAACTTACATATTTAACAattata                                      >  1:544565/1‑131 (MQ=255)
                                                                                             ttACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGTCACAGTGAACTTACCTATTTAACATTTGTCt                                     <  1:24130/134‑1 (MQ=255)
                                                                                               aCTTTTTAGATATTCAACTTTCAACTGAAATAAAAGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGTCACAGTGAACTTACCTATTTAACATTTGTCTAc                                   <  1:123625/134‑1 (MQ=255)
                                                                                                cTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGTCACAGTGACCTTACCTATTTTACTTTTGTCTACa                                  >  1:175962/1‑134 (MQ=255)
                                                                                                 tttttAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGTCACAGTGAACTTACCTATTTAACATTTGTCTACaa                                 >  2:21444/1‑134 (MQ=255)
                                                                                                 tttttAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGCCACAGTGAACTTACCTATTTAACATTTGTCTACaa                                 >  2:344302/1‑134 (MQ=255)
                                                                                                  ttttAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGTCACAGTGAACTTACCTATTTAACATTTGTCTACaaa                                >  1:282563/1‑134 (MQ=255)
                                                                                                      aGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGTCACAGTGAACTTACCTATTTAACATTTGTCTACAAAGATg                            >  2:181353/1‑134 (MQ=255)
                                                                                                         tatTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCCGTTGGTAACATTATTTTCGTTACGAGTCACAGTGAACTTACCTATTTAAAATTTGACTACAAAGTTGCAg                         >  1:6582/1‑134 (MQ=255)
                                                                                                          atTCAACTATCAACCGGGAGAAAGTGTAGCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTCACGAGTCACAGTGAACTTACCTATTTAACATTTGTCTACAAAGTTGCAGc                        <  1:199167/134‑1 (MQ=255)
                                                                                                                   ttgacggATATTAATTGTATCACACTAGGCAGTGAAATTCGTACGCACGACCCAGTTGGTAACATTATCTGCGTTACGAGTCACAGTGAACGTGCCTAGTTAACATTTGTCTACAAAGTTGCGGCGATGGattt               <  2:318500/128‑1 (MQ=255)
                                                                                                                     aactGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGTCACAGACAGCTTACCTATTTAACATTAGTCTACAAAGTTGCAGCGATGGatttta             >  2:396849/1‑134 (MQ=255)
                                                                                                                      actGATATTAATGGTATCAAATTAGGAAGTGAAATTCGTAAGCATGACAGAGTAGGTAAAAATATTTTCGTTACGAGTCACAGTGAACTTACCTATTTAACATTTGTCTACAAAGTTGCAGCGATGGattttat            <  1:103015/134‑1 (MQ=255)
                                                                                                                       ctGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGTCACAGTGAACTTACCTATTTAACATTTGTCTACAAAGTTGCAGCGATGGattttctt           >  2:62790/1‑134 (MQ=255)
                                                                                                                       ctGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGTCACAGTGAACTTACCTATTTAACATTTATCTACAAAGTTGCAGCGATGGattttata           >  1:27722/1‑133 (MQ=255)
                                                                                                                                taggTATCAAATTACGCAATGAAATTCGTAAGCATTACTCAGTAGGCAACATTATTTTCGTTACGAGTCACAGTGAACTTACCTATTTAACATTTGTCTACAAAGTTGCAGCGATGGATTTTATTTTTAAAgat  <  2:36561/132‑1 (MQ=255)
                                                                                                                                  |                                                                                                                                   
AATGATAGAAGAAAAGCCTATGGAAATTGCCCTCGCAACTGATAATCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGTCACAGTGAACTTACCTATTTAACATTTGTCTACAAAGTTGCAGCGATGGATTTTATTTTTAAAGAT  >  USA300TCH1516_ALE/2149692‑2149953

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑