Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 641,194 C→T 12.3% P233L (CCA→CTA)  yhdG_1 → putative amino acid permease YhdG

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE641,1940CT12.3% 98.0 / 3.4 41P233L (CCA→CTA) yhdG_1putative amino acid permease YhdG
Reads supporting (aligned to +/- strand):  ref base C (21/12);  new base T (2/3);  total (25/16)
Fisher's exact test for biased strand distribution p-value = 3.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGTTCATTCTTTGGTAATAATTTTGCACTTGAAAATTTACAACCGTTAGCTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCGTGTACAGTTTATTAGCAGCATCATTAACTTATGTTGTCATGATTTTATACACTGGTTGGTTATCAACAAGTCATCAAAGTTTA  >  USA300TCH1516_ALE/641060‑641330
                                                                                                                                      |                                                                                                                                        
tGGTTCATTCTTTGGTAATAATTTTGCACTTGAAAATTTACAACCGTTAGCTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCGACAAAc                                                                                                                                    >  1:46511/1‑141 (MQ=255)
 ggTTCATTCTTTGGTAATAATTTTGCACTTGAAAATTTACAACCGTTAGCTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTAGCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAAca                                                                                                                                   <  1:119355/141‑1 (MQ=255)
   ttCATTCTTTGGTAATAATTTTGCACTTGAAAATTTACAACCGTTAGCTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAAcagc                                                                                                                                 <  1:213965/141‑1 (MQ=255)
    tCATTCTTTGGTAATAATTTTGCACTTGAAAATTTACAACCGTTAGCTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCTACAAAcagcg                                                                                                                                >  1:47426/1‑140 (MQ=255)
    tCATTCTTTGGTAATAATTTTGCACTTGAAAATTTACAACCGTTAGCTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCTACAAAcagca                                                                                                                                >  1:47422/1‑141 (MQ=255)
     cATTCTTTGGTAATAATTTTGCACTTGAAAATTTACAACCGTTAGCTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAAcagcag                                                                                                                               >  2:326318/1‑141 (MQ=255)
      aTTCGTTGGTAATAGTGGTGCAGTTGAAAATTTACAACCGTTAGCTGAGCCGAGCAAGGGATGGTTAGTGTCTATTGTGGCTATTGTACCCGTCGCACCAGCGGCATAGGTTGGATTTGATAATGTTCTACAAACAGCaga                                                                                                                              <  2:357455/141‑1 (MQ=255)
           ttGGTAATAATTTTGCACTTGAAAATTTACAACCGTTAGCTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGt                                                                                                                         >  1:159385/1‑141 (MQ=255)
           ttGGTAATAATTTTGCACTTGAAAATTTACAACCGTTAGCTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGt                                                                                                                         <  1:100970/141‑1 (MQ=255)
            tGGTAATAATTTTGCACTTGAAAATTTACAACCGTTAGCTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCAACAAACCGCAGAAGAGtt                                                                                                                        >  1:180205/1‑141 (MQ=255)
             ggTAATAATTTTGCACTTGAAAATTTACAACCGTTAGCTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGttt                                                                                                                       <  1:89241/141‑1 (MQ=255)
                aataatTTTGCACTTGAAAATGTACAACCGTTAGCTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCAGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAAc                                                                                                                    >  1:206281/1‑141 (MQ=255)
                   aatTTTGCACTTGAAAATTTACAACCGTTAGCTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACttt                                                                                                                 >  1:54485/1‑141 (MQ=255)
                   aatTTTGCACTTGAAAATTTACAACCGTTAGCCGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACttt                                                                                                                 >  1:293599/1‑141 (MQ=255)
                       ttGCACTTGAAAATTTACAACCGTTAGCTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATAGGTTGGATTTGATAATATTCCACAAACTGCAGCGGAGATTACCTTTGCAc                                                                                                             >  1:142022/1‑141 (MQ=255)
                                aaaaTTTACAACCGTTAGCTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTGTAACTTTGCACCAAACAAGa                                                                                                    >  1:229254/1‑141 (MQ=255)
                                          aCCGTTATGTGAACCTAGCAAAGGATGGTTTGTGTCTATTGTGGTTATTGTATACGTGGCACCAAGGGCATATGTTGGATTTGATAATATTCCACAAACAGCTGAAGAGTTTAACTGTGCACCAAACAAGACATTTAAGCt                                                                                          <  2:90015/141‑1 (MQ=255)
                                             gTTAGCTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTAt                                                                                       <  2:174235/141‑1 (MQ=255)
                                                aGCTGAACCTAGCAAAGGATGGTTAGTGTCGATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCgt                                                                                    <  2:58092/141‑1 (MQ=255)
                                                  cTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCgtgt                                                                                  >  1:355159/1‑141 (MQ=255)
                                                  cTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCgtgt                                                                                  <  1:326318/141‑1 (MQ=255)
                                                            cAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCGTGTACAGttgctt                                                                        >  1:46036/1‑137 (MQ=255)
                                                                   tGGTTAGTGTCTATTGTGGATATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCGTGTACAGTTTATTAgcagca                                                                 >  1:211262/1‑141 (MQ=255)
                                                                            tCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCGTGTGCAGTTTATTCGCAGCATCATTAACt                                                        <  1:200852/141‑1 (MQ=255)
                                                                                  gtgGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCGTGTACAGTTTATTAGCAGCATCATTAACTTAtgtt                                                  >  1:55464/1‑141 (MQ=255)
                                                                                        aTTGTATCCGTGGCACCATGAGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCGTGTACAGTTTATTAACAGCATCATTAACTTATGTTGTCCTg                                            >  1:241352/1‑141 (MQ=255)
                                                                                          tGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAACTTATCGTGTACAGTTTATTAGCAGCATCATTAACTTATGTTGTCATGAt                                          <  2:293599/141‑1 (MQ=255)
                                                                                               ccGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCGTGTACAGTTTATTAGCAGCATCATTAACTTATGTTGTCATGATTTtat                                     >  1:321642/1‑141 (MQ=255)
                                                                                                    gCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCGTGTACAGTTTATTAGCAGCATCATTAACTTATGTTGTCATGATTTTATACACt                                >  1:382843/1‑141 (MQ=255)
                                                                                                     cACCATGGACATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGGTTATCGTGTACAGTTTATTAGCAGCATCATTAACTTATGTTGTCATGATTTTATACACtg                               >  1:223987/1‑141 (MQ=255)
                                                                                                     cACCATGGACATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATCTCAGCTTATCGTGTACAGTTTATTAGCAGCATCATTAACTTATGTTGTCATGATTTTATACACtg                               >  1:290223/1‑141 (MQ=255)
                                                                                                                    ttGGATTTGATAATATTCCACAAACAGCAGAGGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCGTGTACAGTTTATTAGCAGCATCATTAACTTATGTTGTCATGATTTTATACACTGGTTGGTTATcaacaa                >  1:232986/1‑141 (MQ=255)
                                                                                                                    ttGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCGTGTACAGTTTATTAGCAGCATCATTAACTTATGTTGTCATGATTTTATACACTGGTTGGTTATcaacaa                >  2:81966/1‑141 (MQ=255)
                                                                                                                        tgttGATAATATTCACCAAACAGCAGAAGAGTTTACCGTTGCACCAACAAGGACATTTAAGCTTATCGTGTACAGTTTATTAGCAGCATCATTAGCTTATGTTGGCATGATTATGTTCACCGGTTGGTTATCAACAAGtca            <  2:85936/139‑1 (MQ=255)
                                                                                                                        aTTTGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCGTGTACAGTTTATTAGCAGCATCATTAACTTATGTTGTCATGATTTTATACACTGGTTGGTTATCAACAAGtaa            >  1:94722/1‑139 (MQ=255)
                                                                                                                        aTTCGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACAGTTAAGCTTATCGTGTACAGTTTATTAGCAGCATCATTAACTTATGTTGTCATGATTTTATACACTGGTTGGTTATCAACAAGtca            <  2:109881/141‑1 (MQ=255)
                                                                                                                               aataTTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCGTGTACAGTTTATTAGCAGCATCATTAACTTATGTTGTCATGATTTTATACACTGGTTGGTTATCAACAAGTCATACAAGt     >  2:137924/1‑141 (MQ=255)
                                                                                                                                  atTCTACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCGTGTACAGTTTATTAGCAGCATCATTAACTTATGTTGTCATGATTTTATACACTGGTTGGTTATCAACAAGTCATCAAAGttga  <  2:47422/141‑3 (MQ=255)
                                                                                                                                  atTCTACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCGTGTACAGTTTATTAGCAGCATCATTAACTTATGTTGTCATGATTTTATACACTGGTTGGTTATCAACAAGTCATCAAAGTTTa  <  2:47426/141‑1 (MQ=255)
                                                                                                                                  atTCCACCAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCGTGTACAGTTTATTAGCAGCATCATCAACTTCTGTTGTCATGATTTTATACACTGGTTGGTTAACAACAAGTCATCAAAGTTTa  <  1:243255/141‑1 (MQ=255)
                                                                                                                                  atTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCGTGTACAGTTTATTAGCAGCATCATTAACTTATGTTGTCATGATTTTATACACTGGTTGGTTATCAACAAGTCATCAAAGTTTa  >  2:161354/1‑141 (MQ=255)
                                                                                                                                      |                                                                                                                                        
TGGTTCATTCTTTGGTAATAATTTTGCACTTGAAAATTTACAACCGTTAGCTGAACCTAGCAAAGGATGGTTAGTGTCTATTGTGGTTATTGTATCCGTGGCACCATGGGCATATGTTGGATTTGATAATATTCCACAAACAGCAGAAGAGTTTAACTTTGCACCAAACAAGACATTTAAGCTTATCGTGTACAGTTTATTAGCAGCATCATTAACTTATGTTGTCATGATTTTATACACTGGTTGGTTATCAACAAGTCATCAAAGTTTA  >  USA300TCH1516_ALE/641060‑641330

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: ‑