Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,430,220 T→C 10.5% intergenic (+329/‑531) ybiT → / → lysC putative ABC transporter ATP‑binding protein YbiT/Aspartokinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,430,2200TC10.5% 93.8 / 2.4 38intergenic (+329/‑531)ybiT/lysCputative ABC transporter ATP‑binding protein YbiT/Aspartokinase
Reads supporting (aligned to +/- strand):  ref base T (19/15);  new base C (2/2);  total (21/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01

CATTTTCATTCAGTCAACTACTGTCAATATAACATTGCAGGGCCTAGGGCATTGATTCATGTCCGAGACTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACGCATTAAAAGAGTACATTTATTTAATGTGCATATTGATTATGCTATAAGTATTTTGAATTTTATT  >  USA300TCH1516_ALE/1430084‑1430353
                                                                                                                                        |                                                                                                                                     
cATTTTCATTCAGTCAACTACTGTCAATATAACATTGCAGGGCCTAGGGCATTGATTCATGTCCGAGACTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTtttta                                                                                                                                    <  2:350518/140‑1 (MQ=255)
cATTTTCATTCAGTCAACTACTGTCAATATAACATTGCAGGGCCTAGGGCATTGATTCATGTCCGAGACTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTtttta                                                                                                                                    <  2:350335/140‑1 (MQ=255)
   tttCATTCAGTCAACTACTGTCAATATAACATTGCAGGGCCTAGGGCATTGATTCATGTCCGAGACTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCAAGGTGTCCTttttattt                                                                                                                                 >  1:268817/1‑140 (MQ=255)
        ttcaGTCAACTACTGTCAATATAACATTGCAGGGCCTAGGGCATTGATTCATGTCCGAGACTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTTTtgttttattt                                                                                                                            >  2:382163/1‑140 (MQ=255)
        ttcaGTCAACTACTGTCAATATAACATTGCAGGGCCTAGGGCATTGATTCATGTCCGAGACTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCATTTTtatttttttt                                                                                                                            >  2:202268/1‑140 (MQ=255)
                actactGTCAATATAACATTGCAGGGCCTAGGGCATTGATTCATGTCCGAGACTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTCTTATTTTATTTTTTAacac                                                                                                                    >  1:438767/1‑140 (MQ=255)
                actactGTCAATATAACATTGCAGGGCCTAGGGCATTGATTCATGTCCGAGACTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTACTTCTTATTTTATTTTTTAacac                                                                                                                    >  1:438970/1‑140 (MQ=255)
                    ctGTCAATATAACATTGCAGGGCCTAGGGCATTGATTCATGTCCGAGACTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCa                                                                                                                >  1:329418/1‑140 (MQ=255)
                              gaccttGCAGGGCCTAGGGCATTGATTCATGTCCGAGACTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGaa                                                                                                      <  2:244686/136‑1 (MQ=255)
                                cATTGCAGGGCCTAGGGCATTGATTCATGTCCGAGACTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAATGAaca                                                                                                    >  1:437405/1‑140 (MQ=255)
                                 aTTGCAGGGCCTAGGGCATTGATTCATGTCCGAGACTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAacac                                                                                                   <  1:443312/140‑1 (MQ=255)
                                       gggCCTAGGGCATTGATTCATGTCCGAGACTATATTTAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTtc                                                                                             <  1:211890/140‑1 (MQ=255)
                                       gggCCTAGGGCATTGATTCATGTCCGAGACTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATTAGCATAGTGAACACCCCTtc                                                                                             >  2:356985/1‑140 (MQ=255)
                                        ggCCTAGGGCATTGATTCATGTCCGAGACTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGGGTCCTTTTTATTTTATTTTTTAACACATAAGCATAGTGAACACCCCTtct                                                                                            >  2:445315/1‑140 (MQ=255)
                                                         cATGTCCGAGACTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAg                                                                           >  1:194405/1‑140 (MQ=255)
                                                         cATGTCCGAGACTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAg                                                                           >  2:104794/1‑140 (MQ=255)
                                                               cGAGACTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGATAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACAAATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCa                                                                     >  2:201936/1‑140 (MQ=255)
                                                                  gaCTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACg                                                                  <  2:297043/140‑1 (MQ=255)
                                                                       tatTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCGTCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCTGCATAGTGAACACCCCTTTTTTAAATTTCAAATATTGTTATCAAAGCATTa                                                             >  2:184646/1‑140 (MQ=255)
                                                                                tAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACGCATTAAAAGAGTAc                                                    <  1:525598/140‑1 (MQ=255)
                                                                                      aaaTTAACTGGGCCTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACGCATTAAAAGAGTACatttat                                              <  2:455943/138‑1 (MQ=255)
                                                                                          tAACTGGGCGTCTCGATGCTAATATTTATAGCATCGCGGTGTCCTTTTTATTTTATTTTTTAACACATCAACATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCCACGCATTAAACGAGTACattcatttca                                          >  1:9495/1‑138 (MQ=255)
                                                                                          tAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACGCATTAAAAGAGTACATTTATTTaa                                          >  1:153183/1‑140 (MQ=255)
                                                                                              tGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACGCATTAAAAGAGTACATTTATTTAAtgtg                                      <  1:471981/140‑1 (MQ=255)
                                                                                               gggCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACGCATTAAAAGAGTACATTTATTTAATGTGc                                     >  1:269071/1‑140 (MQ=255)
                                                                                               gggCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACGCATTAAAAGAGAAAATTTATTTAATGTGc                                     >  2:124867/1‑140 (MQ=255)
                                                                                                   gtttccaTGCTTATTTTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCTCTTCTCTAAATTACAAATACAGTTATCAACGCATTAAAAGAGTACATTTATTTAATGTGCatat                                 <  2:22663/134‑1 (MQ=255)
                                                                                                     ctcGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATATTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACTCATTAAAAGAGTACATTTATTTAATGTGCATATTg                               >  1:63363/1‑140 (MQ=255)
                                                                                                     cccGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTACTCTAAATTACAAATACAGTTATCAACGCATTAAAAGAGTACATTTATTTAATGTGCATATTg                               <  1:350794/138‑1 (MQ=255)
                                                                                                      ttgATGCTAATATTTATAGCATCGAGGCGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCCTCTCTAAATTACAAATACAGTTATCAACGCATTAAAAGAGTACATTTATTTAATGTGCATATTGa                              <  1:382163/138‑1 (MQ=255)
                                                                                                      tcGATGCTAATACTTACAGCATCGAGGTGTCCTTTTTATCTTATTTTTTAACACATCAGCATAGTGAACACCCCTTTTCTAAATTACTAATACAGTTATCAACGCATTAAAAGAGTACATTTATTTAATGTGCATATTGa                              <  1:467/140‑1 (MQ=255)
                                                                                                                   ttATAGCATCGAGGTGTCCTTCTTATTTTATTTTTTAACACATCCGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACGCATTAAAAGAGTACATTTATTTAATGTGCATATTGATTATGCTATAAGt                 <  2:438970/140‑1 (MQ=255)
                                                                                                                   ttATAGCATCGAGGTGTCCTTCTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACGCATTAAAAGAGTACATTTATTTAATGTGCATATTGATTATGCTATAAGt                 <  2:438767/140‑1 (MQ=255)
                                                                                                                      taGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACGCATTAAAATGTTAGATTTTTTTAAAGTGCATTTTGACTATGCTATATGTAtt              >  1:76398/1‑140 (MQ=255)
                                                                                                                      taGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACGCATTAAAAGAGTACATTTATTTAATGTGCATATTGATTATGCTATAAGTAtt              >  2:205242/1‑140 (MQ=255)
                                                                                                                       aGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACGCATTAAAAGAGTACATTTATTTAATGTGCATATTGATTATGCTATAAGTAttt             >  1:63429/1‑140 (MQ=255)
                                                                                                                       aGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACGCATTAAAAGAGTACATTTATTTAATGTGCATATTGATTATGCTATAAGAAttt             >  1:270601/1‑140 (MQ=255)
                                                                                                                           tCGAGGTGTCCTTTGTATTTTATTTTTTAACACATCAGCATACTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACGCATTAAAAGACTACATTTATTTAATGTGCATATTGATTATGCTATAAGTATTTTGaa         <  1:387974/140‑1 (MQ=255)
                                                                                                                             gAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACGCATTCAAAGAGTACATTTATTTAATGTGCATATTGATTATGCTATAAGTATTTTGAatt       <  1:356985/140‑1 (MQ=255)
                                                                                                                                  gtCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACGCATTAAAAGAGTACATTTATTTAATGTGCATATTGATTATGCTATAAGTATTTTGAattttatt  <  1:539782/140‑1 (MQ=255)
                                                                                                                                  gtCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACGCATTAAAAGAGTACATTTATTTAATGTGCATATTGATTATGCTATAAGTATTTTGAattttatt  <  2:133779/140‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                     
CATTTTCATTCAGTCAACTACTGTCAATATAACATTGCAGGGCCTAGGGCATTGATTCATGTCCGAGACTATATTCAATTTAATAGACATTAACTGGGCGTCTCGATGCTAATATTTATAGCATCGAGGTGTCCTTTTTATTTTATTTTTTAACACATCAGCATAGTGAACACCCCTTCTCTAAATTACAAATACAGTTATCAACGCATTAAAAGAGTACATTTATTTAATGTGCATATTGATTATGCTATAAGTATTTTGAATTTTATT  >  USA300TCH1516_ALE/1430084‑1430353

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: ‑