Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 71,870 T→C 9.1% A368A (GCA→GCG)  arcD_1 ← Arginine/ornithine antiporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE71,8700TC 9.1% 121.5 / 4.2 44A368A (GCA→GCG) arcD_1Arginine/ornithine antiporter
Reads supporting (aligned to +/- strand):  ref base T (21/19);  new base C (2/2);  total (23/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.00e-01

ATCCAGCTGCATAAACCAACCAAATTGTGTAAATAGATGCAATAATTCCTATTATCCATTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAATAACTGAACTAATATATTAGTAATAATTAAAGCGTTGACCGGAGCTTTATTCTTATTTTCTTTAGCAAAC  >  USA300TCH1516_ALE/71731‑72005
                                                                                                                                           |                                                                                                                                       
atcCAGCTGCATAAACAAACCAAATTGTGTAAATAGATGCAATAATTCCTATTATCCATTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGGATTAAGATTg                                                                                                                                        >  1:204705/1‑141 (MQ=255)
    aGCTGCATAAACCAACCAAATTGTGTAAATAGATGCAATAATTCCTATTATCCATTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACt                                                                                                                                    <  1:18955/141‑1 (MQ=255)
     gCTGCATAAACCAACCAAATTGTGTAAATAGATGCAATAATTCCTATTATCCATTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACtt                                                                                                                                   >  2:91906/1‑141 (MQ=255)
         cATAAACCAACCAAATTGTGTAAATAGATGCAATAATTCCTATTATCCATTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATg                                                                                                                               >  1:213014/1‑141 (MQ=255)
                  accaaATTGGGTAAATAGATTCAGTATTTCCTATTATCCATTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGaaa                                                                                                                      <  2:54792/141‑1 (MQ=255)
                     aaaTTGTGTAAATAGATGCAATAATTCCTATTATCCATTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACg                                                                                                                   >  1:178995/1‑141 (MQ=255)
                      aaTTGTGTAAATAGATGCAATAATTCCTATTATCCATTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCCAGTAAAAGCga                                                                                                                  >  2:329544/1‑140 (MQ=255)
                          gtgtACACAGATAGAAGAATACCAACTAGCCATTGCTGTAAATTAGCTTTAGATTTACTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAAc                                                                                                              <  1:155113/141‑1 (MQ=255)
                          gtgtAAATAGATGCAATAATTCCTATTATCCATTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAAc                                                                                                              <  1:301875/141‑1 (MQ=255)
                           tgtAAATAGATGCAATAATTCCTATTATCCATTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACt                                                                                                             <  2:227472/141‑1 (MQ=255)
                           ggtAAATAGATGCAATAATTCCGATTATCCATTGTTCGAAATGTGATTTAAAGTTATTTTGAATAGTATATTAAAAAAAGAAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACt                                                                                                             <  1:338857/140‑1 (MQ=255)
                            gtAAATAGATGCAATAATTCCTATTATCCATTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTg                                                                                                            <  1:329360/141‑1 (MQ=255)
                             tAAATAGATGCAATAATTCCTATTATCCATTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATCGCACTTGATGCAAGTGAAAACGCAAACTGa                                                                                                           >  2:316931/1‑141 (MQ=255)
                             tAAATAGATGCAATAATTCCTATTATCCATTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATCGCACTTGATGCAAGTGAAAACGCAAACTGa                                                                                                           >  2:316915/1‑141 (MQ=255)
                              aaaTAGATGCAATAATTCCTATTATCCATTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGAt                                                                                                          <  2:178995/141‑1 (MQ=255)
                                atggATGCAATAATTCCTTTTATCCATTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACGGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAg                                                                                                        <  2:117868/138‑1 (MQ=255)
                                     tGCAATAATTCCTATTATCCATTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACt                                                                                                   <  1:132286/141‑1 (MQ=255)
                                       cAATAATTCCTATTATCCATTGTTTTAAATTAGCTTTAGAGTTATTTTGAATAGTATATTTAACCCGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAATCTGATATGCACTAt                                                                                                 >  1:246601/1‑141 (MQ=255)
                                       cAATAATTCCTATTATCCATTGTTTTAAATTAGCTTTAGAATTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTAt                                                                                                 >  1:246622/1‑141 (MQ=255)
                                          taatTCCTATTATCCATTGTTTTAAATTAGCTTTAGATTTATTTGGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGCGAAAACGCAAACTGATAGGCACTATCTg                                                                                              >  1:194498/1‑141 (MQ=255)
                                                cTATTATCCATTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAaaca                                                                                        >  1:197030/1‑141 (MQ=255)
                                                         aTTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTaa                                                                               >  2:108004/1‑141 (MQ=255)
                                                          ttGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAAt                                                                              >  1:177068/1‑141 (MQ=255)
                                                              tttAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACCTACTAATTaaa                                                                          >  1:9137/1‑141 (MQ=255)
                                                               ttAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTATAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTaaaa                                                                         <  1:111737/141‑1 (MQ=255)
                                                                tAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTaaaaa                                                                        <  2:234663/141‑1 (MQ=255)
                                                                           tAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAAAATACTAATTAAAAATAACTGAACTa                                                             >  2:123594/1‑141 (MQ=255)
                                                                                  atttgaaaTGGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGAACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAATAACTGAACTAATATAtt                                                      <  2:149176/135‑1 (MQ=255)
                                                                                     ttGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAATAACTGAACTAATATATTAGt                                                   >  1:178844/1‑141 (MQ=255)
                                                                                               tatTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAATAACTGAACTAATATATTAGTAATAATTaaa                                         >  2:314529/1‑141 (MQ=255)
                                                                                                  ttAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAATAACTGAACTAATATATTAGTAATAATTAAAGCg                                      >  1:214134/1‑141 (MQ=255)
                                                                                                  ttAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAATAACTGAACTAATATATTAGTAATAATTAAAGCg                                      >  1:215078/1‑141 (MQ=255)
                                                                                                   tagccTGGTAAAAAGCACTGAGAGTAGATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAATAACTGAACTACTATCTTAGTCATGTTTaaaccat                                     <  2:246601/138‑5 (MQ=255)
                                                                                                         ggTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAATAACTGAACTAATATATTAGTAATAATTAAAGCGTTGACCg                               <  2:15925/141‑1 (MQ=255)
                                                                                                         ggTAAAAAGCACTGAGTGTATATGGAATTAAGATCGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAATAACTGAACTAATATATTAGTAATAATTAAAGCGTTGACCg                               <  1:316931/141‑1 (MQ=255)
                                                                                                         ggTAAAAAGCACTGAGTGTATATGGAATTAAGATCGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAATAACTGAACTAATATATTAGTAATAATTAAAGCGTTGACCg                               <  1:316915/141‑1 (MQ=255)
                                                                                                             aaaaGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAATAACTGAACTAATATATTAGTAATAATTAAAGCGTTGACCGGAGc                           <  1:28641/141‑1 (MQ=255)
                                                                                                                      gAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAATAACTGAACTAATATATTAGTAATAATTAAAGCGTTGACCGGAGCTTTATTCtt                  <  2:161853/141‑1 (MQ=255)
                                                                                                                        gtgtATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAGTAACTGAACTAATATATTAGTAATAATTAAAGCGTTGACCGGAGCTTTATTCTTAt                <  1:263360/141‑1 (MQ=255)
                                                                                                                          gtATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAATAACTGAACTAATATATTAGTAATAATTAAAGCGTTTACCTGAGCTTTATTCTTAttt              >  2:148026/1‑141 (MQ=255)
                                                                                                                            atatGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAATAACTGAACTAATATATTAGTAATAATTAAAGCGTTGACCGGAGCTTTATTCTTATTTTc            <  1:91906/141‑1 (MQ=255)
                                                                                                                               tGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAATAACTGAACTAATATATTAGTAATAATTAAAGCGTTGACCGGAGCTTTATTCTTATTTTCttt         >  1:105862/1‑141 (MQ=255)
                                                                                                                                  aaTTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAATAACTGAACTAATATATTAGTAATAATTAAAGCGTTGACCGGAGCTTTATTCTTATTTTCTTTAGc      >  1:83502/1‑141 (MQ=255)
                                                                                                                                      aaGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAATAACTGAACTAATATATTAGTAATAATTAAAGCGTTGACCGGAGCTTTATTCTTATTTTCTTTAGCAAAc  >  1:97711/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                       
ATCCAGCTGCATAAACCAACCAAATTGTGTAAATAGATGCAATAATTCCTATTATCCATTGTTTTAAATTAGCTTTAGATTTATTTTGAATAGTATATTTAACCTGGTAAAAAGCACTGAGTGTATATGGAATTAAGATTGCACTTGATGCAAGTGAAAACGCAAACTGATAGGCACTATCTGTAAACAACATACTAATTAAAAATAACTGAACTAATATATTAGTAATAATTAAAGCGTTGACCGGAGCTTTATTCTTATTTTCTTTAGCAAAC  >  USA300TCH1516_ALE/71731‑72005

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑