Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,435,068 C→T 22.7% T142I (ACA→ATA)  dapH → 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,435,0680CT22.7% 64.7 / 4.4 39T142I (ACA→ATA) dapH2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase
Reads supporting (aligned to +/- strand):  ref base C (13/15);  new base T (6/3);  total (19/20)
Fisher's exact test for biased strand distribution p-value = 4.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

ACCAGGTGCGTTTATTAGAGAACAAGCCATTATTGAAGATGGTGCTGTCGTTATGATGGGCGCAACAATTAATATTGGCGCAGTCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGTGCTACAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGCTTCACCGGTTATAATCGAGGATGATGTATTAATCGGTGCAAATGCAGTTATTTTAGAAGGTGTACGTGTTGG  >  USA300TCH1516_ALE/1434931‑1435206
                                                                                                                                          |                                                                                                                                          
aCCAGGTGCGTTTATTAGAGAACAAGCCATTATTGAAGATGGTGCTGTCGTTATGATGGGCGCAACAATTAATATTGGCGCAGTCGTTGGCGAAGGTACAATGATCGATATGAATGCTACTCTCGGTGGTCGCGCTACaat                                                                                                                                         >  2:584912/1‑140 (MQ=255)
 ccAGGTGCGTTTATTAGAGAACAAGCCATTATTGAAGATGGTGCTGTCGTTATGATGGGCGCAACAATTAATATTGGCGCAGTCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGTGCTACAACt                                                                                                                                        <  1:621919/141‑1 (MQ=255)
     gTGCGTTTATTAGAGAACAAGCCATTATTGAAGATGGTGCTGTCGTTATGATGGGCGCAACAATTAATATTGGCGCAGTCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGTCCTATCATTGGTa                                                                                                                                    >  2:704179/1‑141 (MQ=255)
     gTGAGTTTAGTATAGAACAAGGCAGTATGGATGATGGTGGTGTCGTTATGATATGCGCAACAATGAATTTTTGGGGGGGCGTTGGCGAAGGTAGAATGATTGATATGAATGCTACTCTCGGTGGTCGTGCTACAACTGGTa                                                                                                                                    <  2:723456/141‑1 (MQ=255)
         gTTTATTAGAGAACAAGCCATTATTGAACATGGTGCTGTCGTTATGATGGGCGCAACAATTAATATTGGCGCAGTCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGTGCTACAACTGGTaaaaa                                                                                                                                <  1:124636/141‑1 (MQ=255)
                  agaACAAGCCATTATTGAAGATGGTGCTGTCGTTATGATGGGCGCAACAATTAATATTGGCGCAGTCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGTTCTATCATTAAAAAAAATATACATGt                                                                                                                       >  2:122142/1‑141 (MQ=255)
                        aGCCATTATTGAAGATGGTGCTGTCGTTATGATGGGCGCAACAATTAATATTGGCGCAGTCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGCCGTATCATTGGAAAAAATCTACATGTAgggcc                                                                                                                 >  2:407598/1‑139 (MQ=255)
                          ccATTATTGAAGATGGTGCTGTCGTTATGATGGGCGCAACAATTAATATTGGCGCAGTCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGTGCTACAACTGGTAAAAATGTACATGTAGGGGCTg                                                                                                               <  1:261418/141‑1 (MQ=255)
                                  gAAGATGGTGCTGTCGTTATGATGGGCGCAACAATTAATATTGGCGCAGTCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGTGCTCCAACTGGTAAACATGTACATGTAGGGGCTGGCGCAGTa                                                                                                       >  1:86661/1‑141 (MQ=255)
                                     gATGGTGCTGTCGTTATGATGGGCGCAACAATTAATATTGGCGCAGTCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGTGCTACAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTa                                                                                                    <  1:225073/141‑1 (MQ=255)
                                        ggTGTTGTAGGTATGATGGTAGCAAAAATTAAGAGTGGAGCGGTCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGTGCTACAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCa                                                                                                 <  2:114645/141‑1 (MQ=255)
                                        ggTGCTGTCGTTATGATGGGCGCAACAATTAATATTGGCGCAGTCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGTGCTACAACTGGTAAAAAGGTACAGGTAGGGGCTGGGGCTGtggtggcg                                                                                                 >  1:100519/1‑134 (MQ=255)
                                         gTGCTGTCGTTATGATGGGCGCAACAATTAATATTGGCGCAGTCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGTGCTACAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAg                                                                                                >  1:695578/1‑141 (MQ=255)
                                           gCTGTCGTTATGATGGGCGCAACAATTAATATTGGCGCAGTCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGTGCTACAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGgt                                                                                              >  1:322908/1‑141 (MQ=255)
                                            cTGTCGTGATGATGGGCGCAACAATTAATATTGGCGCAGTCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGTGCTACAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGgtg                                                                                             <  1:496132/141‑1 (MQ=255)
                                                cattgtgatgaACGCAACAAGTTCTATCGGCCCAGTGGTTGGCGAAGGTACAACGACTGATATCAATGCTACTCTCGGTGGTCGTGCTACAACTGGTAAAAATGTATATGTACGGCCTGGCGCAGTATTAGCAGGTGTCAt                                                                                         <  2:224802/136‑1 (MQ=255)
                                                     tgatgGGCGCAACAATTAATATTGGCGCAGTCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGCAGTATCATTGGTAAAAATATACATGTAGGGGCTGCCGCAGTATTATGAGCTATGATTGAAc                                                                                    >  2:513138/1‑141 (MQ=255)
                                                               aacaaTTAATATTGGCGCAGTCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGCCGTATCATTAAAAAAAAAATACATGTAGGGGCTGGCGCAGTATTAGCAAGAGAAATAGAAACCCCTAGTGc                                                                          >  2:388803/1‑141 (MQ=255)
                                                               aacaaTTAATAGTGGCGCAGTCGTTGGCGAAGGTATAATGATTGATATGAATACTACTCTCGGTGGTCGTGCTATAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGc                                                                          <  2:49191/141‑1 (MQ=255)
                                                                  aaTTAATATTGGCGCAGTCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGTGCTACAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGCTTc                                                                       >  1:617640/1‑141 (MQ=255)
                                                                          ttGGCTCAATCGTTGGCTAAGGTACAATGATTGATATGAATGCTGCTACGCTCGATCGTGGTATTACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGCTTCACCGGTta                                                               <  2:566494/141‑1 (MQ=255)
                                                                            ggCGCAGTCGTTGGCGAAGGTACAATGAGTGATATGAATGCTACTCTCGGTGGTCGTGCTACAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGCTTCACCGGTtata                                                             <  1:407598/141‑1 (MQ=255)
                                                                                 aGTCGGTGGAGAAGGTAAAATGATGGAGATGAATGCTAGTCTCGGTGGTCGTGGTACAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGCTTCACCGGTTATAATCGa                                                        <  1:185295/141‑1 (MQ=255)
                                                                                   tCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGTGCTACAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGCTTCACCGGTTATAATCGAgg                                                      >  1:117994/1‑141 (MQ=255)
                                                                                     gTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGTGCTACAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGCTTCACCGGTTATAATCGAGgat                                                    <  2:5584/141‑1 (MQ=255)
                                                                                                    aTGATTGATATGAATGCTACTCTCGGTGGTCGCCGTACAATTAAAAAAAAAATACATGTAGGGGCTGGCGCAGTATTAGCAGGAATGATTGAACCCCCTAGTGCTTCACCGGTTATAAACAAGGATGATGTATTAATCAGt                                     >  2:244055/1‑141 (MQ=255)
                                                                                                     tgattgatATGAATGCTACTCTCGGTGGTCGTGCTACAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGCTTCACCGGTTATAATCGAGGATGATGTATTAATCGGTg                                    <  1:704179/141‑1 (MQ=255)
                                                                                                               gAATGCTACTCTCGGTGGTCGTGCTACAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGCTTCACCGGTTATAATCGAGGATCATGGAAGAGTCGGTGCAAATGCAGt                          >  1:102110/1‑141 (MQ=255)
                                                                                                                 aTGCTACTCTCGGTGGTCGCCGTATCATTAAAAAAAAAATACATGTAGGGGCTGGCGCAGTATTAGAAGGTGTGATTGAACCCCCTAGTGCTTCACCGGTTATAAACGCCAAAAAGTTATTAATCGCAGCACACGCAGTTa                        >  2:3849/1‑141 (MQ=255)
                                                                                                                     tACTCTCGGTGGTCGTGCTACAACTGGTAAAAATGTACATGCGTGGGCTGGTGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGCTTCACCGGTTATAATCGAGGATGATGTATTAATCGGTGCAAATGCAGTTAtttt                    <  1:585975/141‑1 (MQ=255)
                                                                                                                     gaCTCTCGGTGGTCGTGATTCAACCGGGAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGCTTCACCGGTTATAATCGAGGATGATGTATTAATCGGTGCAAATGCAGTTAtttt                    <  1:668589/140‑1 (MQ=255)
                                                                                                                       ctctCGGTGGTCGTGCTACAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGCTTCACCGGTTATAATCGAGGATGATGTATTAATCGGTGCAAATGCAGTTATTTTAg                  >  1:167596/1‑141 (MQ=255)
                                                                                                                         ctcGGTGGTCGTGCTACAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGCTTCACCGGTTATAATCGAGGATGATGTATTAATCGGTGCAAATGCAGTTATTTTAGaa                >  1:645822/1‑141 (MQ=255)
                                                                                                                              tttgtCGTGTTATAAGTTGTAAAAATGTACAGGTAGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGCTTCACCGGTTATAATCGAGGATGATGTATTAATCGGTGCAAATGCAGTTATTTTAGAAGgtg            <  1:159561/138‑1 (MQ=255)
                                                                                                                              tggtCGTGCTACAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGCTTCACCGGTTATAATCGAGGATGATGTATTAATCGGTGCAACTGCAGTTATTTTAGACGgtgt           >  1:243162/1‑141 (MQ=255)
                                                                                                                              gcggtCGAGCGACAGATGGTAAAAATGTGCAAGAAGGGGCTGGGGTGGGATTAGGAGGTGTGATGGAACCCTATAGGACTTCGCCGATTATAAGCGAGGATGAAGGATTAATCGGTGCAAATGCAGTGATTTTAGAAGgtg            <  2:327294/139‑1 (MQ=255)
                                                                                                                                gggcGTGATAGAACTGGTAAAAATGGATATGTGGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACACTCTAGTGCTTCACCGGTTATAATCGAGGATGATGTATTAATCGGTGCAAATGCAGTTCTGATAGAATGTGTa          <  2:662139/138‑1 (MQ=255)
                                                                                                                                   ggTGCTAAAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGCTTCACCGGTTATAATCGAGGATGATGTATTAATCGGTGCAAATGCAGTTATTTTAGAAGGTGTACgt       <  2:614442/140‑1 (MQ=255)
                                                                                                                                        tACAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGCTTCACCGGTTATAATCGAGGATGATGTATTAATCGGTGCAAATGCAGTTATTTTAGCAGGTGTAGCTGTTgg  >  2:191662/1‑141 (MQ=255)
                                                                                                                                          |                                                                                                                                          
ACCAGGTGCGTTTATTAGAGAACAAGCCATTATTGAAGATGGTGCTGTCGTTATGATGGGCGCAACAATTAATATTGGCGCAGTCGTTGGCGAAGGTACAATGATTGATATGAATGCTACTCTCGGTGGTCGTGCTACAACTGGTAAAAATGTACATGTAGGGGCTGGCGCAGTATTAGCAGGTGTGATTGAACCCCCTAGTGCTTCACCGGTTATAATCGAGGATGATGTATTAATCGGTGCAAATGCAGTTATTTTAGAAGGTGTACGTGTTGG  >  USA300TCH1516_ALE/1434931‑1435206

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: