Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,373,697:1 +T 20.0% coding (79/1335 nt) pbuG ← Guanine/hypoxanthine permease PbuG

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,373,6971.T20.0% 59.9 / 16.2 25coding (79/1335 nt)pbuGGuanine/hypoxanthine permease PbuG
Reads supporting (aligned to +/- strand):  ref base . (8/12);  new base T (2/3);  total (10/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAATATCATTCTTAATAAAAAAC  >  USA300TCH1516_ALE/2373559‑2373835
                                                                                                                                           |                                                                                                                                          
tGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTGAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑Ta                                                                                                                                          >  2:197627/1‑141 (MQ=255)
tGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑tt                                                                                                                                          <  1:74134/141‑2 (MQ=255)
       cGAGCCTACGAATGCTGCTAATGCAGTCGTGACAAAAATGGCATCTTGGTCCATTTTCATATCATCTGATACGCCTTGAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGt                                                                                                                                   <  2:276683/141‑1 (MQ=255)
         cgCCTACAGATGCTGCTAATGCAGTCGCTACAAAACTGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTtg                                                                                                                                 <  2:221752/140‑1 (MQ=255)
                        ctAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGATTAAGAAAGTTGTGATACCGCCTAAg                                                                                                                   >  1:107046/1‑141 (MQ=255)
                         tAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGATTAAGAAAGTTGTGATACCGCCTAAGa                                                                                                                  <  2:269778/141‑1 (MQ=255)
                            tGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTtc                                                                                                              <  1:75813/141‑1 (MQ=255)
                                   tcTACAAACATGGTACCTTGGTTCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAGAGTTGTGATACCGCCTAAGATTTCTCTTTTa                                                                                                       <  2:109262/140‑1 (MQ=255)
                                    cTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGCTTTCTCTTTTaa                                                                                                      >  1:111827/1‑141 (MQ=255)
                                       cAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAg                                                                                                    >  2:324528/1‑141 (MQ=255)
                                           aaTGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGt                                                                                               <  1:321048/141‑1 (MQ=255)
                                            aTGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTGAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGtt                                                                                              <  1:197627/141‑1 (MQ=255)
                                                                cATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCAATAGA‑TAAGAAAGTTGTGATACCACATAAGATTTCTATTTTAAAGTTTGTTTCATATTTATCGAACttgta                                                                          >  2:316253/1‑137 (MQ=255)
                                                                        ctGAGACGCCTGTAACATCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGtttt                                                                  <  1:159146/141‑1 (MQ=255)
                                                                              cGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTACGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAATTTTTCACGa                                                            >  1:82/1‑141 (MQ=255)
                                                                               gCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGTCTAAGATTTCTCTTTTAAAGTTTGTTTCATATTTATCGAACTGAAAATAGTTTTTCACGaa                                                           >  2:178711/1‑141 (MQ=255)
                                                                                    tAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGGTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCTATATTTATCGAACTGGAAATAGTTTTTTGCGTATggtt                                                      >  1:61128/1‑139 (MQ=255)
                                                                                            gCTAAACTTAAAACGTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCttt                                              <  1:27252/141‑1 (MQ=255)
                                                                                             cTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGATTAAAAACATGGGGGTACCGCCTAAGATTTTTCGTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCttt                                              <  1:324528/141‑1 (MQ=255)
                                                                                              tAAACTTAAGACCTGCAGGTTGACTGCTAAAATATAGGCCATAGA‑TAAGAGAGTGGTGATACCGGCTAAGATTTCTCTTTGAGAGTTTGTGCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCttttt                                            <  2:343316/141‑1 (MQ=255)
                                                                                              tAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCttttt                                            <  1:123214/141‑1 (MQ=255)
                                                                                              tAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCttttt                                            <  1:114158/141‑1 (MQ=255)
                                                                                                            gCGGGCTAACTGCTAAAATATAGGCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTa                               <  1:226229/141‑1 (MQ=255)
                                                                                                             cGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCGAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAAt                             <  1:119221/141‑1 (MQ=255)
                                                                                                                       gCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAatat                   >  1:218027/1‑141 (MQ=255)
                                                                                                                                        aGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTTTTTTTTTTTTATAGTTTAATATCATTCTTAATATAAAAc  >  2:231455/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                          
TGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAATATCATTCTTAATAAAAAAC  >  USA300TCH1516_ALE/2373559‑2373835

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: ‑