Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,557,393 A→G 29.1% D281G (GAT→GGT)  garK_2 → Glycerate 2‑kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,557,3930AG29.1% 53.0 / 29.4 53D281G (GAT→GGT) garK_2Glycerate 2‑kinase
Reads supporting (aligned to +/- strand):  ref base A (11/25);  new base G (7/8);  total (19/34)
Fisher's exact test for biased strand distribution p-value = 3.41e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.86e-01

ATAAGATAAAAATGTGCACAGGAAAGTCCGTTAATCAAATACCAGGTTCTGGTGCAGCTGGCGGTATGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTATCAGACCATCTTTGGTAAAACACCCGTAGGCGTTGCGTTAGCTGCAAAACAATATCATATTCCTGTCATCGCGATTTG  >  USA300TCH1516_ALE/2557255‑2557531
                                                                                                                                          |                                                                                                                                          
ataagataaAAATGTGCACAGGAAAGTCCGTTAATCAAATACCAGGTTCTGGTGCAGCTGGCGGTATGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGAt                                                                                                                                           <  2:41052/140‑1 (MQ=255)
ataagataaAAATGTGCACAGGAAAGTCCGTTAATCAAATACCAGGTTCTGGTGCAGCTGGCGGTATGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGAt                                                                                                                                           >  1:396165/1‑140 (MQ=255)
   agataaAAATGTGCACAGGAAAGTCCGTTAAGCAAATACCAGGTTCTGGTGCAGCTGGCGGTATGGGCGCAGCATTATTAGCGTTTTTTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGAtttt                                                                                                                                        <  2:189279/140‑1 (MQ=255)
   agataaAAATGGGCCCAGTAGAGTGCGTTAATCAAATGCCAGGTTCTGGTGCAGCTGTCGGTATGGGCTCAGCATTTTTATCTTTTTGTGACACAACTTTAACAAAGGTTATTGAAGTCGTCTTTGATATTACAGAtttt                                                                                                                                        <  2:269546/140‑1 (MQ=255)
     cgaaaaaCTTGCACATGACAGTCCGTGAAGCAAATACCGGGTTCTGGTGCAGCCGTCTGTATGGGCCCAGCGTGATTAGCGGTCTGTTAGACTACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATTTcca                                                                                                                                      <  2:19030/138‑1 (MQ=255)
     ataaAAATGTGCACAGGAAAGTCCGTTAATCAAATACCAGGTTCTGGTGCAGCTGGCGGTATGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGCttttaa                                                                                                                                      >  2:31924/1‑138 (MQ=255)
       aaaaaTGTGCACAGGAAAGTCCGTTAATCAAATACCAGGTTCTGGTGCAGCTGGCGGTATGGTCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGGTCTtcatc                                                                                                                                    <  2:593297/140‑1 (MQ=255)
        aaaaTGTGCACAGGAAAGTCCGTTAATCAAATACCAAGTTCTGGTGCAGCTGGCGGTATGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAAGTTTtcatca                                                                                                                                   >  2:439046/1‑140 (MQ=255)
         aaaTGTGCACAGGAAAGTCCGTTAATCAAATACCAGGTTCTGGTGCAGCTGGCGGTATGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGCCATTACAGATTTTCATCaa                                                                                                                                  <  1:522844/140‑1 (MQ=255)
         aaaGGTGCAAAGGAAAGTCCGTTAATCAAATACCAGGTTCTGGTGCAGCTGGCGGTATGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATTTTCATCaa                                                                                                                                  <  2:10900/140‑1 (MQ=255)
              tgCACAGGAAAGTCCGTTAATCAAATACCAGGTTCTGGTGCAGCTGGCGGTATGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATTTGCATCAAAGAAt                                                                                                                             >  1:582382/1‑140 (MQ=255)
                       aaGTCCGTTAATCAAATACCAGGTTCTGGTGCAGCTGGCGGTATGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATCTTCATCAAAGAATTAAAGATGc                                                                                                                    <  2:486932/140‑1 (MQ=255)
                          accGTTAATCAAACACCAGGTTATGGTCCAGCTGGCGGTATGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATTTTCATCAAAGAATTAAAGATGCata                                                                                                                 <  2:1820/139‑3 (MQ=255)
                            cGTTAATCCACTACCCGGTTCTGGTGCCGCTGGCGGTCAGGGCGCAACACTGTACCCTTTTTTTGAGACAACTTTAACAAAATGTATTGATGTTGTCTTTGACATTACAGGTTTTCATCAAAGAATTAAAGATGCAGAcc                                                                                                               <  2:303128/140‑1 (MQ=255)
                                          cAGGATCTGGTGCAGCTGGTGGGATGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAGAAGGGATTGATGTCGTCTTTGACATGACAGATTTTCATCAAAGAAGTAAAGATGCCGACCTCGCTCTTACTGga                                                                                                 >  2:312221/1‑140 (MQ=255)
                                           acacgttGGTGCAGCTGGCGGTATGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTTgag                                                                                                >  2:336046/7‑140 (MQ=255)
                                           aGGTTCTGGTGCAGATGGCGGTATGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGACGTCTTTGACATGACAGGTTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGgag                                                                                                >  2:456009/1‑140 (MQ=255)
                                            gtttCTCGGGCAGCTGGTGGTATGGGAGCAGCATTATTAGCGGTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGgaga                                                                                               <  2:506524/138‑1 (MQ=255)
                                                  ggTGCAGCTGGCGGTATGGGCGGAGCATTATTAGCGTATTGTGAGACAACTTTAACAAAAGGTATTGAGGTCGGCTGTGCCCTTACAGATTTTCGTCAAAGAATTAAAGATGCAGACCTCGTCATTACTGGAgacggacg                                                                                         >  2:400615/1‑140 (MQ=255)
                                                    gggaggtggtggTGTGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATTTGCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCa                                                                                       <  2:47332/134‑1 (MQ=255)
                                                       aGCTGGCGGTATGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGGTTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATgg                                                                                    <  1:391731/140‑1 (MQ=255)
                                                         ttGGCGGGTTGGGCTCATCATTATTAGCGTTTTGTGAGATAACTTTAACAAAAGGTATTTATGGCGTCTTTGACATTACAGATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGAt                                                                                  <  2:347643/139‑1 (MQ=255)
                                                         cTGGCGGTATGGGCTCAGTATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGAt                                                                                  <  2:380691/140‑1 (MQ=255)
                                                          tGGCGGTATGGGCGCAGCATTATTTGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGAtt                                                                                 <  2:344221/140‑1 (MQ=255)
                                                          tGGCGGTATGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGCTGTCGTCTTTGACATTACAGATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGAtt                                                                                 >  2:456407/1‑140 (MQ=255)
                                                           ggCGGTATGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGGTTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTa                                                                                >  1:52277/1‑140 (MQ=255)
                                                           ggCGGTATGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTa                                                                                >  2:562414/1‑140 (MQ=255)
                                                            gCGGTATGGGCTCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTAt                                                                               <  1:309627/140‑1 (MQ=255)
                                                             cGGTATGGGCGCAGCATTATTAGCGTTCTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTATc                                                                              <  1:636869/140‑1 (MQ=255)
                                                                 aggggCGCAGCATTATTAGCTTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATCTTCACCCCCGACGGAAAGATGCAGTAATCGGTTTTACTGGAGAAGGACGCATGGATTAGCAGAc                                                                          <  2:469960/138‑1 (MQ=255)
                                                                    ggtccagaaTTAGTAGCGTTTTGTGAAACAACTTTAACAAAAGGTATTGAGGTCGTCTTTTACATTACAGGTTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTATCAGACCAt                                                                       <  1:281698/136‑1 (MQ=255)
                                                                            attattAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTATCAGACCATCTTTGGTa                                                               <  2:156276/140‑1 (MQ=255)
                                                                             ttattaGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGCCATTACAGATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTATCCGACCATCTTTGGTac                                                              >  2:567411/1‑139 (MQ=255)
                                                                              tattaGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGCATATCAGAACATCTTTGGTaaa                                                             >  2:44867/1‑140 (MQ=255)
                                                                               atgaGCGTTTTGTGAGACAACTTTAACAACAGGTATTGATGTCGTCTTTGACATGACAGCTTTTCGTCAAAGCATTAAAGATGCATCCCTCGTTATTACCGGAGAAGGACGCATGGATTATCAGACCATCTTAGGTaaaa                                                            <  2:422399/137‑1 (MQ=255)
                                                                                     gTTTTGTGAAACAACTTTAACAAAAGGTATTGAGGTCGTCTTTGACAATACAGGTTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTATCAGACCATCTTTGGTAAAACACCCg                                                      >  2:427771/1‑140 (MQ=255)
                                                                                      ttttGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATTTTCATCAAAGAATTAAAGATGCGGACCTCGTTATTACTGGAGAAGGACGCATGGATTATCAGACCATCTTTGGTAAAACACCCGt                                                     >  2:537182/1‑140 (MQ=255)
                                                                                            gagaCAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGGTTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTATCAGACCATCTTTGGTAAAACACCCGTAGgcgt                                               >  1:37281/1‑140 (MQ=255)
                                                                                                 aaCTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTATCAGACCATCTTTGGTACAACACCCGTAGgcgttgcgt                                          <  1:420967/140‑1 (MQ=255)
                                                                                                    tttAACAAAAGTTATTGTTGTCGTCTTTGACATTACTGGTTTTCATCTAATAATTGAAGATGTAGACGTCGTTATTACTGGAGAAGGACGCATGGATTGTCCGAGCAGCGTTGTTAAACCACCCGTAGtcgttgcttttt                                       <  2:172100/140‑3 (MQ=255)
                                                                                                     ttAACAAAAGGGATTGAGGGGGTCTTTGACATTACAGATCTGCAGCACTTAATTAAAGACCCAGACCTCGTTATCCCTGGAGAAGGACGCAGGTATTATCACACCATCTTTTGTAAAACACCCGTAGGCGTTGCGTTAGc                                      <  2:221206/140‑1 (MQ=255)
                                                                                                        aCAAAAGGGATTGATGTCGTCTTTGACATTACAGATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTATCAGACCATCTTTGGTAAAACACCCGTAGGCGTTGCGTTAGCTGc                                   <  2:396165/140‑1 (MQ=255)
                                                                                                                     aTGTCGTCTTTGACATTACAGGTTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTCCTGGAGAAGGACGCATGGATTATCAGACCATCTTTGGTAAAACACCCGTAGGCGTTGCGTTAGCTGCAAAACAATATCat                      <  2:158705/140‑1 (MQ=255)
                                                                                                                        tcgtcTTTGACATTTTTGATTTTCATCAAAGATTTTAAGCTTCAGACCTCGTTATTACTGTAGAAGGACGCATGGATTATCAGACCTTTTTTGGTTTAACACCCGTAGGCGTTGCGTTAGCTGCAAAACAATATCATAtt                   <  2:454398/140‑1 (MQ=255)
                                                                                                                           tcTTTGACATTACAGGTTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTATCAGACCATCTTTGGTAAAACACCCGTAGGCGTTCCGTTAGCTGCAAACCAATATCATATTcat                >  1:31304/1‑138 (MQ=255)
                                                                                                                              ttGACATTACAGGTTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGAATGGATTATCAGACTTTCTTTGGTAAAACACCCGTAGGCGTTGCGTTAGCTGCAAAACAATATCATATTCCTggc             >  2:401796/1‑138 (MQ=255)
                                                                                                                               tGACATTACAGATTTCCAGCAATGAATTAAAGATGCATATCTCGTTATTACTGGAGAAGGACGCATGGATTATCAGACCATCTTTGTTAAAACACCCGTAGGCGTTGCGTTAGCTGCAAAACAATATCATATTCCTGTCa            <  1:563525/140‑1 (MQ=255)
                                                                                                                                gACATTACAGATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTATCAGACCATCTTTGGTAAAACACCCGTAGGCGTTGCGTTAGCTGCAAAACAATATCATATTCCTGTCAt           <  1:562414/140‑1 (MQ=255)
                                                                                                                                 aCATTACAGGTTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTATCAGACCATCTTTGGTAAAACACCCGTAGGCGTTGCGTTAGCTGCAAAACAATATCATATTCCTGTCATc          <  1:105528/140‑1 (MQ=255)
                                                                                                                                  cATTACAGGTTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTATCAGACCATCTTTGGTAAAACACCCGTAGGCGTTGCGTTAGCTGCAAAACAATATCATATTCCTGTCATcg         <  1:389069/140‑1 (MQ=255)
                                                                                                                                   atgaCAGATTTTCATCAAAGTATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTATCAGACCATCTTTGGTAAAACACCCGTAGGCGTTGCGTTAGCTGCAAAACAGTATCATATTCCTGTCATcgc        <  1:169302/137‑1 (MQ=255)
                                                                                                                                       cAGATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTATCAGACCATCTTTGGTAAAACACCCGTAGGCGTTGCGTTAGCTGCAAAACAATATCATATTCCTGTCATCGCGAtt    <  2:176196/140‑1 (MQ=255)
                                                                                                                                         gATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTATCAGACCATCTTTGGTAAAACACCCGTAGGCGTTGCGTTAGCTGCAAAACAATATCATATTCCTGTCATCGCGCttgt  >  2:318553/1‑138 (MQ=255)
                                                                                                                                          |                                                                                                                                          
ATAAGATAAAAATGTGCACAGGAAAGTCCGTTAATCAAATACCAGGTTCTGGTGCAGCTGGCGGTATGGGCGCAGCATTATTAGCGTTTTGTGAGACAACTTTAACAAAAGGTATTGATGTCGTCTTTGACATTACAGATTTTCATCAAAGAATTAAAGATGCAGACCTCGTTATTACTGGAGAAGGACGCATGGATTATCAGACCATCTTTGGTAAAACACCCGTAGGCGTTGCGTTAGCTGCAAAACAATATCATATTCCTGTCATCGCGATTTG  >  USA300TCH1516_ALE/2557255‑2557531

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: ‑