Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 299,913 T→A 8.7% H60Q (CAT→CAA)  USA300HOU_0266 → 2‑C‑methyl‑D‑erythritol 4‑phosphate cytidylyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730299,9130TA 8.7% 125.0 / 4.2 46H60Q (CAT→CAA) USA300HOU_02662‑C‑methyl‑D‑erythritol 4‑phosphate cytidylyltransferase
Reads supporting (aligned to +/- strand):  ref base T (19/23);  new base A (2/2);  total (21/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.78e-01

ACGTACCTTTACCTAAACAATTTTTAGATTTAGACAACAAACCGATTTTAATCCATACATTAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAACGATACAATTATGAATATCGTTAAACATATTGAATCAACAAATGGTATTAACGATGACGAT  >  CP000730/299783‑300048
                                                                                                                                  |                                                                                                                                       
aCGTACCTTTACCTAAACAATTTTTAGATTTAGACAACAAAACGATTTTAATCCATACATTAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATGATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATa                                                                                                                               <  2:2300/141‑1 (MQ=255)
      cTTTACCTAAACAATTTTTAGATTTAGACAACAAACCGATTTTAATCCATACATTAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTa                                                                                                                         >  1:19000/1‑141 (MQ=255)
         tACCTAAACAATTTTTAGATTTAGACAACAAACCGATTTTAATCCATACATTAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGaa                                                                                                                      >  1:197029/1‑141 (MQ=255)
                    tttttAGATTTAGACAACAAACCGATTTTAATCCATACATTAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAAAAATGGATGACGCATACGAAAGATACACTTAGAAAATGCAAAAtt                                                                                                           >  1:123906/1‑141 (MQ=255)
                     ttttAGATTTAGACAACAAACCGATTTTAATCCATACATTAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTCAGAAAATTCAAAAttt                                                                                                          <  1:170280/141‑1 (MQ=255)
                     ttttAGAATAAGACAACAAACAGATCTTAATTCATACTTGAGAAAAATTTATTTTAATTGATGATTTTGAAAAAATTATTATTGCGACGCCACAACAATGGATGACGCATCCGAAAGATACTCTTAGAAAATTCAAAAttt                                                                                                          <  2:106615/141‑1 (MQ=255)
                        tagatttagaCAACAAACCGATTTTAATCCATACATTAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCtg                                                                                                       >  2:182174/1‑141 (MQ=255)
                        tagatttagaCAACAAACCGATTTTAATCCATACATTAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCAAACGAAAGATACACTTAGAAAATTCAAAATTTCtg                                                                                                       >  1:320260/1‑141 (MQ=255)
                        tagatttagaCAACAAACCGATTTTAATCCATACATTAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCAAACGAAAGATACACTTAGAAAATTCAAAATTTCtg                                                                                                       >  1:335728/1‑141 (MQ=255)
                              tagaCAAAAAACCGATTTTAATCCATACGTTAGAAAAATTTACTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGaaa                                                                                                 <  1:324962/141‑1 (MQ=255)
                                gaCAACAAACCGATTTTAATCCATACATTAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGa                                                                                               <  1:294561/141‑1 (MQ=255)
                                     caaACCGATTTTAATCCATACATTAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAAAAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGa                                                                                          >  2:94585/1‑141 (MQ=255)
                                       aaCCGATTTTAATCCATACATTAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAg                                                                                        <  1:116478/141‑1 (MQ=255)
                                           gATTTTAATCCATACATTAGAAAAGTTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAACGATACACGTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCAt                                                                                    <  2:215524/141‑1 (MQ=255)
                                              tttAATCCATACATTAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGGCGCCACAACAATGGATGACGCATATGAAAGATACACTTAGAAAATTCAAACTTTCTGATGAAAGAATTGAAGTCATTCa                                                                                 <  1:222578/141‑1 (MQ=255)
                                              tttAATCCATACATTAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATAGGAAAGATACACTTAGAAAATTCAAATTTTCTGATGAAAGAATTGAAGTCATTCa                                                                                 <  1:222967/141‑1 (MQ=255)
                                                 aaTCCATACATTAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAgg                                                                              >  2:55630/1‑141 (MQ=255)
                                                    ccATACAATAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAggtgg                                                                           <  2:341685/141‑1 (MQ=255)
                                                       aaCATTAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAg                                                                        <  2:19000/140‑1 (MQ=255)
                                                           ttAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAAAAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTATCGAt                                                                    >  2:79913/1‑141 (MQ=255)
                                                             aGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCg                                                                  <  2:248055/141‑1 (MQ=255)
                                                             aGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCg                                                                  <  1:336941/141‑1 (MQ=255)
                                                                aaaaTTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTaa                                                               <  2:129922/141‑1 (MQ=255)
                                                                 aaaTTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAAc                                                              >  2:259086/1‑141 (MQ=255)
                                                                   atttatttTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAACGa                                                            <  2:81436/141‑1 (MQ=255)
                                                                      tatttTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAGATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAACGATAc                                                         <  2:316833/141‑1 (MQ=255)
                                                                      tatttTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAACGATAc                                                         <  2:303519/141‑1 (MQ=255)
                                                                      tatttTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCAAACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAACGATAc                                                         <  2:320260/141‑1 (MQ=255)
                                                                      tatttTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCAAACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCAATCGTAGCGAtcc                                                         <  2:335728/141‑3 (MQ=255)
                                                                       atttTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGTTAGCGATCGTAACGATACa                                                        <  1:182174/141‑1 (MQ=255)
                                                                       atttTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTAAAGGTGGTAGCGATCGTAACGATACa                                                        >  2:142362/1‑141 (MQ=255)
                                                                        ttttAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATGGTAACGATACaa                                                       >  2:220645/1‑141 (MQ=255)
                                                                         tttAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAACGATACAAt                                                      <  2:200464/141‑1 (MQ=255)
                                                                                   aaTTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAACGATACAATTATGAATATc                                            <  2:136874/140‑1 (MQ=255)
                                                                                         gAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAACGATACAATTAGGAATCACGTTaaa                                      >  2:189272/1‑141 (MQ=255)
                                                                                            aaaaTTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAACGATACAATTATGAATATCGTTAAACaa                                   >  2:234215/1‑140 (MQ=255)
                                                                                             aaaTTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAACGATACAATTATGAATATCGTTAAACata                                  >  1:85385/1‑141 (MQ=255)
                                                                                                ttattaTCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAACGATACAATTATGAATATCGTTAAACATATTg                               >  1:6295/1‑141 (MQ=255)
                                                                                                  attatCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAGTTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGGTCGTAACGATACACATATGAATATAGTTAAACATATGGat                             >  1:71856/1‑140 (MQ=255)
                                                                                                   ttatCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAACTATACAATTATGAATATCGTTAAACATATTGTAt                            >  1:234572/1‑141 (MQ=255)
                                                                                                       cgcgACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAACGATACAATTATGAATATCGTTAAACATATTGAATcaac                        <  2:197611/141‑1 (MQ=255)
                                                                                                            cGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAACGATACAATTATGAATATCGTTAAACATATTAAATCAGCAAATg                   >  2:9351/1‑141 (MQ=255)
                                                                                                             gCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAACGATACAATTATGAATATCGTTAAACATATTGAATCAACAAATgg                  >  1:234016/1‑141 (MQ=255)
                                                                                                                      aTGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAACGATACAATTATGAATATCGTTAAACATATTGAATCAACAAATGGTATTAacga         <  1:94585/141‑1 (MQ=255)
                                                                                                                       tGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAACGATACAATTATGAATATCGTTAAACATATTGAATCAACAAATGGTATTAacgat        >  1:36787/1‑141 (MQ=255)
                                                                                                                             aagCATAAGAAAGATACACTTAGAAAATTCAAAATTTCTGATTAAAGAATTGAGGTCATTCAAGGTGGTAGCGATCGTAACGATACAATTATGAATATCGTTAAACATATTGAATCATGTTTGACTATTAacgatgacgat  <  2:123906/139‑1 (MQ=255)
                                                                                                                                  |                                                                                                                                       
ACGTACCTTTACCTAAACAATTTTTAGATTTAGACAACAAACCGATTTTAATCCATACATTAGAAAAATTTATTTTAATTAATGATTTTGAAAAAATTATTATCGCGACGCCACAACAATGGATGACGCATACGAAAGATACACTTAGAAAATTCAAAATTTCTGATGAAAGAATTGAAGTCATTCAAGGTGGTAGCGATCGTAACGATACAATTATGAATATCGTTAAACATATTGAATCAACAAATGGTATTAACGATGACGAT  >  CP000730/299783‑300048

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑