Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 385,617 G→A 21.7% H332Y (CAT→TAT)  licR ← putative licABCH operon regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE385,6170GA21.7% 94.9 / 18.3 53H332Y (CAT→TAT) licRputative licABCH operon regulator
Reads supporting (aligned to +/- strand):  ref base G (25/16);  new base A (8/4);  total (33/20)
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

CGTTGAAGCGAATAGCAGCATCTTGTTCAATTGGACTAATATGCTTGCTAACGGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATGCCTAATTCTTGGCTAACACAAGTGATCAATTCATGTATATTTTGCGATAAATCATGGTATTCAAAG  >  USA300TCH1516_ALE/385485‑385747
                                                                                                                                    |                                                                                                                                  
aattGAAGCAAATAGAAGCATCTTGTTCCAGGGGGCAAACAAGCAAGAGAACTGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTTAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGt                                                                                                                                   <  1:14589/132‑1 (MQ=255)
 gTTGAAGCGAAGAGCAGCATCTTGTTCAATTGGACGAAGATGCTGGCTAACGGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGta                                                                                                                                  <  1:583235/134‑1 (MQ=255)
  tggaggCGAATAGCAGCATCTTGTTCAATTGGACTAAGATGCTTGCTAACGGCTTCAATGATTGGGGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGatatat                                                                                                                                 <  2:365472/129‑1 (MQ=255)
   tGAAGCGAATAGCAGCATCTTGTTCAATTGGACTAATATGCTTGCTAACGGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTCTTTAATACGATGtata                                                                                                                                >  2:481330/1‑134 (MQ=255)
           aTAGCAGCATCTTGTTCAATTGGACTAATATGCTTGCTAACGGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGttt                                                                                                                        >  1:257369/1‑134 (MQ=255)
           aTAGCAGCATCTTGTTCAATTGGACTAATATGCTTGCTAACGGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGCttt                                                                                                                        >  1:123246/1‑134 (MQ=255)
                  caTCTTGTTCAATTGGACTAATATGCTTGCTAACGGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATTGTATTTAATACGATATATAGCTGATTTGCTAtgt                                                                                                                 >  1:561546/1‑134 (MQ=255)
                       ttttCAATTGGACTCATATGCTTGCTAACGTCTTCAATGATTTGAGGATAGCGTCGCATAACTTCTTGCCTCAATGGATTAGGTTGTAGCTTATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGAt                                                                                                            <  2:48349/132‑1 (MQ=255)
                        gTTCAATTGGACTAATATGCTTGCTAACGGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATATATAGCTGGTTTGTTATGTGTGATc                                                                                                           >  2:480851/1‑134 (MQ=255)
                        gTTCAATTGGACTAATATGCTTGCTAACGGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATATATAGCTGGTTTGGTATGTGTGATc                                                                                                           >  2:537238/1‑134 (MQ=255)
                               tGGAGTAATATGCTTGCTTAGGGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTACGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTgg                                                                                                    <  1:207811/134‑1 (MQ=255)
                               tGGACTAATATGCTTGGTAACGGCTGCAATGATTTGAGGATAGCGACGCATAACTTCTTTCCTTAAAGGATTAGTTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTgg                                                                                                    <  2:223670/134‑1 (MQ=255)
                                 gACTAATATGCTTGCTAACGGCTTCAATGATTTGAGGATAGAGAGGCATAACTTCTTGACTCCCAGGATTAGGTTGTAGCATATCGTATTTATTACGATGTATAGCTGGTTTGTTATGTTTGATCAGTGTGGTa                                                                                                  >  1:509905/1‑134 (MQ=255)
                                  aCTAATATGCTTGCTAACGGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTGTGATATGTGTGATCAGACTGGTAt                                                                                                 >  2:252586/1‑134 (MQ=255)
                                     aaTATGCTTGCTAACGGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTa                                                                                              >  2:380693/1‑134 (MQ=255)
                                       tatGCTTGCTAACGGCTTCAAGGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAAc                                                                                            >  2:530812/1‑134 (MQ=255)
                                          gcttgctAACGGCTTCAATGATTTGAGGATAGCGACGCATCACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACttg                                                                                         <  2:293106/134‑1 (MQ=255)
                                          gcttgctAACGGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACttg                                                                                         >  1:104946/1‑134 (MQ=255)
                                           cgtgctAACGTCTTTAATGTTGTGAGGCTAGCGACGCATAACTTCTTGCCTCAAATTATTAGGTTGTAGCATTTCTTCTTCAATACGTTATATAGCTGGTTTGATATGTGTGATCAGACTGTTATGTAACttgt                                                                                        <  2:195650/132‑1 (MQ=255)
                                            ttgctAACGGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACttgtt                                                                                       >  1:424358/1‑134 (MQ=255)
                                             tgctGACTGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACttgttg                                                                                      <  2:49188/134‑1 (MQ=255)
                                             tgctAACGGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACttgttg                                                                                      <  2:570377/134‑1 (MQ=255)
                                             tgctAACGGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACttgttg                                                                                      >  2:310250/1‑134 (MQ=255)
                                                  aCGGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGTTTTGATATGTGTGATTAGACTGGTATGTAAATAGTTGTCttt                                                                                 >  1:193317/1‑134 (MQ=255)
                                                     gCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGa                                                                              >  1:460187/1‑134 (MQ=255)
                                                           aTGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATATATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATc                                                                        >  1:54829/1‑134 (MQ=255)
                                                                ttGAGTATAGCTACGCATAACTTCTTTCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATGc                                                                   <  2:175284/134‑1 (MQ=255)
                                                                ttGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTGATACGATGTCAAGCTTGTTTGATATGTGTGATCAGACTGGTATGTAAATTGTTGTATTTTGACATAACAATga                                                                   >  1:307174/1‑133 (MQ=255)
                                                                ttGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATGCGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATAAATGc                                                                   >  2:396316/1‑134 (MQ=255)
                                                                ttGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGCCTGGTATGTACCTTGTTGTCCTTTTACATATCAAtac                                                                   >  1:169876/1‑132 (MQ=255)
                                                                ttGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACATATTGTCTTTTGACATATCAATGc                                                                   >  1:46104/1‑134 (MQ=255)
                                                                ttGAGGATAGCGACGCATAACATCTTGCCGCAAAGGGTTAGGTTGTAACATATCGAATTTAATACGATGTATAGCTGGTTTGATATGAGTGATACGACTGGTATGTACCTTGTTGGCTTTTCGGATATCAATGc                                                                   >  2:120498/1‑134 (MQ=255)
                                                                             agCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTCATACGATGTAGAGCTCGTTTGATCTGTGTGATCAGACTGGTATGTAACTTGCAATCTTTTCACATATCAATGCCTAATTCTTGTCt                                                      >  2:409004/2‑134 (MQ=255)
                                                                              gCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCATATTGGTATGTCACTTGTTGTCTTTTGACCTTTCACTGCCTACTTCCTGCCTa                                                     >  1:95927/1‑134 (MQ=255)
                                                                              gCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATGCCTAATTCTTGGCTa                                                     >  1:234126/1‑134 (MQ=255)
                                                                               cATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATATATAGCTGGTTTGATATGCGTGCTCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATAGCTAATTCTTGGCTaa                                                    >  1:245414/1‑134 (MQ=255)
                                                                                   aCTTCTTTCCTTAGAGGATTAGGTTGTAGCATATCGTATTTAATACGATATATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATGCCTAATTCTTGGCTAAcaca                                                <  1:242313/134‑1 (MQ=255)
                                                                                    cttcttGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATGCCTAATTCTTGGCTAACACaa                                               >  2:339044/1‑134 (MQ=255)
                                                                                             tCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATGCCTGATTCTTGGCTATCACCAGTGGTCTAt                                      >  1:44090/1‑134 (MQ=255)
                                                                                                  ggATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGGTTGATCAGACTGGTATGTAACTTTTTGGCTTTTGACAGATCAATGCCTAATTCTTGGCTAACACAAGTGATCAATTCATg                                 <  2:77504/134‑1 (MQ=255)
                                                                                                   gATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATGCCTAATTCTTGGCTAACACAAGTGATCAATTCATGt                                <  2:115090/134‑1 (MQ=255)
                                                                                                          ttGTAGCATATCGTATTTAATACGATATATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCGATGCCTAATTATTGGCGAACACAAGTGATCAATTCACGTATGtttt                         >  2:34377/1‑134 (MQ=255)
                                                                                                           tGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATGCCTAATTCTTGGCTAACACAAGTGATCAATTCATGTATATTTTg                        <  2:460187/134‑1 (MQ=255)
                                                                                                               gCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATGCCTAATTCTTGGCTAACACAAGTGATCAATTCATGTATATTTTGCGAt                    <  2:234126/134‑1 (MQ=255)
                                                                                                                        aTTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATGCCTAATTCTTGGCTAACACAAGTGATCAATTTATGTATATTTTGCGATAAATCATgg           >  1:440946/1‑134 (MQ=255)
                                                                                                                        aTTTAATACGATATATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATGCCTAATTCTTGGCTAACACAAGTGATCAATTCATGTATATTTTGCGATAAATCATgg           <  2:54829/134‑1 (MQ=255)
                                                                                                                        aTTTAATACGATACATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATGCCTAATTCTTGGCTAACACAAGTGATCAATTCATGTATATTTTGCGATAAATCATgg           <  1:92302/134‑1 (MQ=255)
                                                                                                                         tttAATACGATATATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATGCCTAATTCTTGGCTAACACAAGTGATCAATTCATGTATATTTTGCGATAAATCATGGt          >  2:502701/1‑134 (MQ=255)
                                                                                                                          ttAGTACGATGTATCGTTGGTTTTATATGTGTTATCAGACTTGTATGTAACTTGTTGTCTTTTGACATATCAATGCCTAATTCTTGGCTAACACAAGTGATCAATTCATGTATATTTTGCGATAAATCATGGTa         <  2:89025/134‑1 (MQ=255)
                                                                                                                          ttAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATGCCTAATTCTTGGCTAACACAAGTGATCAATTCATGTATATTTTGCGATAAATCATGGTa         <  1:560173/134‑1 (MQ=255)
                                                                                                                               aCGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATGCCTAATTCTTGGCTAACACAAGTGATCAATTCATGTATATTTTGCGATAAATCATGGTATTCaa    >  2:529252/1‑134 (MQ=255)
                                                                                                                               aCGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATGCCTAATTCTTGGCTAACACAAGTGATCAATTCATGTATATTTTGAGATAAATCATGGTAtataa    >  1:607277/1‑130 (MQ=255)
                                                                                                                                cGATATATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATGCCTAATTCTTGGCTAACACAAGTGATCAATTCATGTATATTTTGCGATAAATCATGGTATTCaaa   >  1:512751/1‑134 (MQ=255)
                                                                                                                                 gATGTATCTGTGGTTTTATACGTGTTATCAGACTGGTATGTAACTTGTTTTCTTTTGACATATCAATGCCTAATTCTTGGCTAACACAAGTGATCAATTCATGTATATTTTGCGATAAATCATGGTATTCAAAg  <  2:139403/134‑1 (MQ=255)
                                                                                                                                    |                                                                                                                                  
CGTTGAAGCGAATAGCAGCATCTTGTTCAATTGGACTAATATGCTTGCTAACGGCTTCAATGATTTGAGGATAGCGACGCATAACTTCTTGCCTCAAAGGATTAGGTTGTAGCATATCGTATTTAATACGATGTATAGCTGGTTTGATATGTGTGATCAGACTGGTATGTAACTTGTTGTCTTTTGACATATCAATGCCTAATTCTTGGCTAACACAAGTGATCAATTCATGTATATTTTGCGATAAATCATGGTATTCAAAG  >  USA300TCH1516_ALE/385485‑385747

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: ‑