Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 860,576 C→T 10.0% S19S (AGC→AGT)  gpmI → 2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE860,5760CT10.0% 103.2 / 3.3 40S19S (AGC→AGT) gpmI2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase
Reads supporting (aligned to +/- strand):  ref base C (12/24);  new base T (2/2);  total (14/26)
Fisher's exact test for biased strand distribution p-value = 6.02e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.70e-01

TGATATTGATGGGGCATTAGTAGGTGGCGCATCACTTAAAGTTGAAGATTTCGTACAATTGTTAGAAGGTGCAAAATAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAACGACTCAAATCGAAGCGAGTGGCTTAGATGTTGGACTACCTGAAGGACAAATGGGTAACTCAGAAGTTGG  >  USA300TCH1516_ALE/860439‑860713
                                                                                                                                         |                                                                                                                                         
tGATATTGATGGGGCATTAGTAGGTGACGCATCACTTAAAGTTGAAGATTTCGTACAATTGTTAGAAGGTGCAAAATAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTCTTGCGAACCGCGAAAGCGaa                                                                                                                                        <  1:239683/141‑1 (MQ=255)
   tatTGATGGTGCATTAGTAGGTAGCGCATCACTTAAAGTTGAAGATTTCGTACAATTGTTAGAAGGTGCAAAATAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACAt                                                                                                                                     <  1:86760/141‑1 (MQ=255)
             gCATTAGTAGGTGGCGCATCACTTAAAGTTGAAGATTTCGTACAATTGTTAGAAGGTGCAAAATAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGCAAGCGAACATGGTAATGAgg                                                                                                                           >  2:394838/1‑141 (MQ=255)
              cactagcagGTGGCGCCTCAATTAAAGTTGAAGAATTCGCACAATTGTTAGCAGGTGCAAAATAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGt                                                                                                                          <  1:179427/138‑1 (MQ=255)
                        gggCGCATCACTTAAAGTTGAAGATTTCGTACAATTGTTAGAAGGTGCAAAATAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCa                                                                                                                <  1:12725/140‑1 (MQ=255)
                                cACTTAAAGTTGAAGATTTCGTACAATTGTTAGAAGGTGCAAAATAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGcc                                                                                                        <  2:388454/141‑1 (MQ=255)
                                cACTTAAAGTTGAAGATTTCGTACAATTGTGAGAAGGTGCAAAATAATCATGGCTAAGAAACCAACTGCGGTAATTATTTTAGATCGATATCCTAACCGCATGGGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGcc                                                                                                        <  2:156305/141‑1 (MQ=255)
                                     aaaGTTGAAGATTTCGTACTATTGTTAGAAGGTGCAAAATAATCATGGCTAAGAAACCACCTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAAtt                                                                                                   <  1:26557/141‑1 (MQ=255)
                                         ttGAAGATTTCGTACAATTGTTAGAAGGTGCAAAATAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGa                                                                                               >  2:392021/1‑141 (MQ=255)
                                          tGAAGATTTCGTACAATTGTTAGAAGGTGCAAAATAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGAt                                                                                              <  1:193830/141‑1 (MQ=255)
                                            aaGATTTCGTACAATTGTTAGAAGGTTCAAAATAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCg                                                                                            <  2:12130/141‑1 (MQ=255)
                                                 ttCGTACAATTGTTAGAAGGTGCAAAATAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGttatt                                                                                       <  1:262868/141‑1 (MQ=255)
                                                       cAATTGTTAGAAGGTGCAAAATAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTacaaca                                                                                 <  1:25604/141‑1 (MQ=255)
                                                            gTTAGAAGGTGCAAAATAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTCATTCGGTTAAGTTAGCAAACAAGCCGAATTTTGATCGTGATTACAACAActat                                                                            >  1:74473/1‑141 (MQ=255)
                                                                 atggTGCAAAATAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAAc                                                                       <  1:98925/139‑1 (MQ=255)
                                                                 aaGGTGCAAAATAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGTGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAAc                                                                       >  1:299563/1‑141 (MQ=255)
                                                                 aaGGTGCAAAATAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGTGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAAc                                                                       >  1:299594/1‑141 (MQ=255)
                                                                   ggTGCAAAATAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAGACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAACGa                                                                     >  1:328290/1‑141 (MQ=255)
                                                                         aaaTAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTACAACAAACATCCACCGACGCaaa                                                               >  2:233156/1‑141 (MQ=255)
                                                                             aatCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACCAGCTTAATTTTGATCGTTATTACAACAAATATCCAACGACTCAAATCGa                                                           <  1:308538/141‑1 (MQ=255)
                                                                             aatCATGGCTAAGAAACCAACNGNGTTNATTATTTTAGATGGTCTTGCGCACCGCGAAAGCGAACATGGTAATGCGGTAAAATTGGCAAACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAACGACTCAAATCGa                                                           <  1:225682/141‑1 (MQ=255)
                                                                               tCATGGCTAATAAACGAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAACGACTCAAATCGAAg                                                         <  2:21138/141‑1 (MQ=255)
                                                                               acATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAACGACTCAAATCGAAg                                                         <  1:175973/140‑1 (MQ=255)
                                                                                cATGGCTAAGAATCCAACTGCGTTAATTATTTGAGATGGTTTTGCGAACCGCGAAAGCGACCGTGGTAGTGCGGTAAAATTTGCTAACGAGACTAATGTTGTTCGTTATTACAACAAATATCCTACGACTCAAATCGAAGc                                                        <  2:112431/141‑1 (MQ=255)
                                                                                cATGGCGAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAACGACTCAAATCGAAGc                                                        <  2:305274/141‑1 (MQ=255)
                                                                                     caaaaaaaCCAACTGCTTTAATTATTTTAGATGGTGTTCCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATGTTGATCGTTATTACAACAAATATCCAACGACTCAAATCGAAGCGAGTg                                                   <  2:131050/136‑1 (MQ=255)
                                                                                       aaGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAACGACTCAAATCGAAGCGAGTGGc                                                 <  1:18912/141‑1 (MQ=255)
                                                                                           aaCCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAACGACTCAAATCGAAGCGAGTGGCTTAg                                             <  1:353386/141‑1 (MQ=255)
                                                                                            aCCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTCTTACAACAAATATCCAACGACTCAAAACCAAGCGAGTGGccaaga                                            >  2:339113/1‑136 (MQ=255)
                                                                                                             ttttAGATGGTTCTGCGAACCGCGAAAGCGAACATGGTACCGCGGTAAAATTAGCAAGCAAGCCTAATTTTGATCGTTATTACAACAAATCTCCACCGACTCAAATCGAAGCGAGGGGCTTAGATGTTGGACTACCTGAAg                           <  2:74473/141‑1 (MQ=255)
                                                                                                               ttAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAACGACTCAAATCGAAGCGAGTGGCTTAGATGTTGGACTACCTGAAGGa                         >  1:293722/1‑141 (MQ=255)
                                                                                                                      gTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAGACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAACGACTCAAATCGAAGCGAGTGGCTTAGATGTTGGACTCCCTGCAGGACAAATgg                  >  2:255666/1‑141 (MQ=255)
                                                                                                                      gTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTACAACAAATATCAAACAACTCAAATCGAAGAGAGGGGCTTAGATGTTGGACTACCTGCAGGCCACATgg                  >  2:39459/1‑141 (MQ=255)
                                                                                                                                ccGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGGTAGTTAGTACCACAAACAGCCAACGACTCAAATCGAAGCGAGTGGGTTAGATGTTGGACTACCTGAAGGACAAATGGGTAACTCAGa        >  1:189722/1‑141 (MQ=255)
                                                                                                                                 cgcgAAAGTGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAACGACTCAAATCGAAGCGAGTGGCTTAGATGTTGGACTACCTGAAGGACAAATGGGTAACTcggta       <  2:299563/141‑5 (MQ=255)
                                                                                                                                 cgcgAAAGTGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAACGACTCAAATCGAAGCGAGTGGCTTAGATGTTGGACTACCTGAAGGACAAATGGGTAACTCAGaa       <  2:299594/141‑1 (MQ=255)
                                                                                                                                  gcgAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAACGACTCAAATCGAAGCGAGTGGCTTAGATGTTGGACTACCTGAAGGACAAATGGGTAACTCAGAAg      <  1:200753/141‑1 (MQ=255)
                                                                                                                                  gcgAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAACGACTCAAATCGAAGCGAGTGGCTTAGATGTTGGACTACCTGAAGGACAAATGGGTAACTCAGAAg      <  1:5215/141‑1 (MQ=255)
                                                                                                                                      aaGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAACGACTCAAATCGAAGCGAGTGGCTTAGATGTTGGACTACCTGAAGGACAAATAGGTAACTCAGAAGGTgg  >  2:4959/1‑141 (MQ=255)
                                                                                                                                      aaGCGAACATAGTAATGCGGTTAAATTAGCAACCCAGCCTAATGTTGATCGTTATTACAACAAATATCCAACGACTCAAATCGAAGAAAGTGCTTTAGCTGTGTCACTACCGGAAGGACAAAGAGGTAACTCAGAAGTTgg  >  2:179680/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                         
TGATATTGATGGGGCATTAGTAGGTGGCGCATCACTTAAAGTTGAAGATTTCGTACAATTGTTAGAAGGTGCAAAATAATCATGGCTAAGAAACCAACTGCGTTAATTATTTTAGATGGTTTTGCGAACCGCGAAAGCGAACATGGTAATGCGGTAAAATTAGCAAACAAGCCTAATTTTGATCGTTATTACAACAAATATCCAACGACTCAAATCGAAGCGAGTGGCTTAGATGTTGGACTACCTGAAGGACAAATGGGTAACTCAGAAGTTGG  >  USA300TCH1516_ALE/860439‑860713

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑