Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,407,273 A→G 8.0% T315T (ACA→ACG)  trpD2 → Anthranilate phosphoribosyltransferase 2

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,407,2730AG 8.0% 131.9 / 3.5 50T315T (ACA→ACG) trpD2Anthranilate phosphoribosyltransferase 2
Reads supporting (aligned to +/- strand):  ref base A (26/20);  new base G (2/2);  total (28/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.10e-01

AATTTAGCAATCTCCCTTAATATCTTGAATGGTAAAGATCAGTCAAGTCGACGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCACTTTTACAAAATGGCTATTATCAAGACAAACTTAATACCTTGAAAA  >  USA300TCH1516_ALE/1407133‑1407413
                                                                                                                                            |                                                                                                                                            
aaTTTAGCAATCTCCCTTAATATCTTGAATGGTAAAGATCAGTCAAGTCGACGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACa                                                                                                                                              >  1:71210/1‑141 (MQ=255)
aaTTTAGCAATCTCCCTTAATATCTTGAATGGTAAAGATCAGTCAAGTCGACGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACa                                                                                                                                              <  1:374671/141‑1 (MQ=255)
        aaTCTCCCTTAATATCTTGAATGGTAAAGATCAGTCAAGTCGACGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACAttgattga                                                                                                                                      <  1:338975/141‑1 (MQ=255)
               cTTAATATCTTGAATGGTAAAGATCAGTCAAGTCGACGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGt                                                                                                                               >  1:210019/1‑141 (MQ=255)
                ttgagatCTTGAATGGTAAAGATCAGTCAAGTCGACGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGATATATAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAATTACATTGATTGATAATGGTg                                                                                                                              <  2:353957/136‑1 (MQ=255)
                ttAATATCTTGAATAGTAAAGATCAGTTAAGTCGAAGTGATGTTGTCTTACTAAATGCAGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTg                                                                                                                              <  2:48366/141‑1 (MQ=255)
                   atatCTTGAATGGTAAAGATCAGTCAAGTCGACGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAg                                                                                                                           >  2:46204/1‑141 (MQ=255)
                       cTTGAATGGTAAAGATCAGTCAAGTCGACGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCAtt                                                                                                                       >  1:605185/1‑141 (MQ=255)
                         tGAATGGTAAAGATCAGTCAAGTCGACGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTgg                                                                                                                     >  2:463238/1‑141 (MQ=255)
                            aTGGTAAAGATCAGTCAAGTCGACGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGaaa                                                                                                                  >  1:186808/1‑141 (MQ=255)
                              ggTAAAGATCAGTCAAGTCGACGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGaaaaa                                                                                                                >  2:512390/1‑141 (MQ=255)
                                 aaaGATCAGTCAAGTCGACGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATAc                                                                                                             >  1:87515/1‑141 (MQ=255)
                                   aGATCAGTCAAGTCGACGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATCATCGTGAAGCATTGGAAAAATACCa                                                                                                           >  2:333979/1‑141 (MQ=255)
                                       cAGTCAAGTCGATGAGCTGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCaa                                                                                                       <  1:399754/141‑1 (MQ=255)
                                         gTCAAGTCGTCGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAAt                                                                                                     <  2:594978/141‑1 (MQ=255)
                                           cAAGTCGACGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATga                                                                                                   <  1:80457/141‑1 (MQ=255)
                                           cAAGTCGACGTAGTGGTGTCGTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATga                                                                                                   <  2:272518/141‑1 (MQ=255)
                                             aGTCGACGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTACGTAGCAGATAAAGGGGATAAAAATAAATAATGCATAGAACTTGCAACTACATTGATTGATAGTGGTGAAGCATTGGAAAAATACCATCAAATgaga                                                                                                 <  1:570195/141‑1 (MQ=255)
                                               tCGACGTGATTTTGTCTTACTAGATCTGGGTTTAAGCCTTTACGTTGCACCGACAGTGCATACTATCGCAGTAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGTATTGGAAAAATACCATCAAATGAGAgg                                                                                               <  2:22218/141‑1 (MQ=255)
                                               tCGACGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAgg                                                                                               >  1:460195/1‑141 (MQ=255)
                                                cGACGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGt                                                                                              <  1:125222/141‑1 (MQ=255)
                                                       aTGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCACAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATAACAACAAATAAGAGGTAaataat                                                                                       >  2:180931/1‑141 (MQ=255)
                                                        tgttgtCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACTATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAataata                                                                                      <  2:250765/141‑1 (MQ=255)
                                                             tCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTTCAACTACATTGATTCATAATGGTTAATCATTGGAAACATACCCTCAAATGACAGATCAATAATTTGAcc                                                                                 >  2:120089/1‑140 (MQ=255)
                                                             tCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATgcag                                                                                 >  1:195489/1‑138 (MQ=255)
                                                               ttACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGAGAATAATATGACGaa                                                                               >  2:437526/1‑140 (MQ=255)
                                                                       tGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAg                                                                       <  2:186808/141‑1 (MQ=255)
                                                                        gCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGa                                                                      >  1:493797/1‑141 (MQ=255)
                                                                            gTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAAtt                                                                  >  1:547019/1‑141 (MQ=255)
                                                                                    cTTTATGTTGCAGAGAAAGTGGATCCCATCGCAGAATGCATAGAACTTGCAACTACATTGCTTGATAATGGTGACGAATTGCAAAACTACCATCAAATGAGAGGAGAATACTATCACGATTCTCTCAGACATTGTCGAata                                                          >  1:288346/1‑141 (MQ=255)
                                                                                         tGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACGTTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAAc                                                     >  1:410869/1‑141 (MQ=255)
                                                                                         tGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACGTTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAAc                                                     >  1:373157/1‑141 (MQ=255)
                                                                                         tGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTACAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAAGTGAATAATATGACGATTTTATCAGAAATTGTAAAATATAAAc                                                     >  2:198877/1‑141 (MQ=255)
                                                                                           ttGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAg                                                   >  1:56506/1‑141 (MQ=255)
                                                                                           ttGAAGAGAAAGTGGATAACAGCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAg                                                   <  2:586499/141‑1 (MQ=255)
                                                                                             gCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTc                                                 >  1:112171/1‑141 (MQ=255)
                                                                                                 agaAAGTGGATACCATAGCAGAAGGAATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTGATCAGAAATTGTTAAATATAAACAGTCACtt                                             <  1:120089/141‑1 (MQ=255)
                                                                                                   aaaGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCACtttt                                           >  1:486723/1‑141 (MQ=255)
                                                                                                    aaGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCACTTTTa                                          >  2:627649/1‑141 (MQ=255)
                                                                                                    aaGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCACTTTTa                                          >  1:533446/1‑141 (MQ=255)
                                                                                                     aGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCACTTTTAc                                         <  2:399917/141‑1 (MQ=255)
                                                                                                               aacGCAGAAGCCAGACAACATGCAACTACAATGATGGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGAGTTTATCAGAAATTGTTAAATATAAACAGTCACTTTTACAAAATGGCta                               <  1:116154/139‑1 (MQ=255)
                                                                                                                   cAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCACTTTTACAAAATGGCtattat                           <  2:16896/141‑1 (MQ=255)
                                                                                                                   cAGAAGGCATAGAACTTGAAACTACATTGATGTATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCACTTTTACAAAATGGCtattat                           <  2:244369/141‑1 (MQ=255)
                                                                                                                       aGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCACTTTTACAAAATGGCTATTATCAAg                       >  2:562988/1‑141 (MQ=255)
                                                                                                                       aGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCACTTTTACAAAATGGCTATTATCAAg                       >  2:58965/1‑141 (MQ=255)
                                                                                                                         gaaTAGAACTGGGAAGTACATTGATTGATAAGGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCACTTTTACAAAATGGCTATTATCAAGAc                     <  2:381399/139‑1 (MQ=255)
                                                                                                                              gAACTTGCAACTACGTTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCACTTTTACAAAATGGCTATTATCAAGACAAACt                <  2:373157/141‑1 (MQ=255)
                                                                                                                              gAACTTGCAACTACGTTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCACTTTTACAAAATGGCTATTATCAAGACAAACt                <  2:410869/141‑1 (MQ=255)
                                                                                                                                aCTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCACTTTTACAAAATGGCTATTATCAAGACAAACTTa              >  1:369256/1‑141 (MQ=255)
                                                                                                                                   tGCCACTACATTGATTGATAAGTGCGAAGCATTGGAAAAATACCAGCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCACTTTTACAAAATGGCTATTATCAAGACAAACTTAATa           <  1:217788/141‑1 (MQ=255)
                                                                                                                                    gCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCACTTTTACAAAATGGCTATTATCAAGACAAACTTAATAc          >  2:392856/1‑141 (MQ=255)
                                                                                                                                            attgattgATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCACTTTTACAAAATGGCTATTATCAAGACAAACTTAATACCTTGaaaa  <  1:76315/141‑1 (MQ=255)
                                                                                                                                            attgattgATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCACTTTTACAAAATGGCTATTATCAAGACAAACTTAATACCTTGaaaa  <  1:357843/141‑1 (MQ=255)
                                                                                                                                            attgattaATAATGGTGAAGCATTGGAACAACACCACCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCAGTTTTACAAAATGGCTATTATCAAGACAAACTTAATACCTTGaaaa  <  1:31928/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                            
AATTTAGCAATCTCCCTTAATATCTTGAATGGTAAAGATCAGTCAAGTCGACGTGATGTTGTCTTACTAAATGCGGGTTTAAGCCTTTATGTTGCAGAGAAAGTGGATACCATCGCAGAAGGCATAGAACTTGCAACTACATTGATTGATAATGGTGAAGCATTGGAAAAATACCATCAAATGAGAGGTGAATAATATGACGATTTTATCAGAAATTGTTAAATATAAACAGTCACTTTTACAAAATGGCTATTATCAAGACAAACTTAATACCTTGAAAA  >  USA300TCH1516_ALE/1407133‑1407413

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: ‑