Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 584,121 G→T intergenic (+205/‑67) rplA → / → rplJ 50S ribosomal protein L1/50S ribosomal protein L10

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE584,1210GT93.9% 92.8 / ‑2.0 33intergenic (+205/‑67)rplA/rplJ50S ribosomal protein L1/50S ribosomal protein L10
Reads supporting (aligned to +/- strand):  ref base G (0/2);  new base T (17/14);  total (17/16)
Fisher's exact test for biased strand distribution p-value = 2.27e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACAATAAGTAATTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCGTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCAAA  >  USA300TCH1516_ALE/583977‑584249
                                                                                                                                                |                                                                                                                                
aCAATAAGTAATTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTggg                                                                                                                              >  1:30095/1‑149 (MQ=255)
                aaGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCtttttt                                                                                                              <  1:234172/149‑1 (MQ=255)
                                  tgATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAg                                                                                            >  2:242152/1‑149 (MQ=255)
                                               tAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTa                                                                               >  1:174605/1‑149 (MQ=255)
                                                  gACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAAt                                                                            >  1:185193/1‑149 (MQ=255)
                                                   aCAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATg                                                                           >  2:206983/1‑149 (MQ=255)
                                                                   ataACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGAAAAAAAAATTTAAATGGAGGTGTCTGAATGTc                                                           <  2:84008/149‑1 (MQ=255)
                                                                    taACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCt                                                          >  1:10938/1‑149 (MQ=255)
                                                                    taACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCt                                                          >  1:144872/1‑149 (MQ=255)
                                                                       attAAAATTTATCCTGGGGCGGTTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGACTTGGGTAGAAAGTGCTTTTTTTAATAATATAAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCt                                                       <  2:152126/148‑1 (MQ=255)
                                                                         tAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTTTTTTTTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTAt                                                     >  2:132640/1‑149 (MQ=255)
                                                                         tAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTAt                                                     <  1:232312/149‑1 (MQ=255)
                                                                         tAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTAt                                                     <  2:154222/149‑1 (MQ=255)
                                                                         tAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTAt                                                     <  2:276128/149‑1 (MQ=255)
                                                                          aaaaTTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTAGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATc                                                    <  2:271658/149‑1 (MQ=255)
                                                                            catctATCCTGCCGAGGCTAAAATTGACTTGCACGTGATGCTCTACGATCTTTCAAGCACTTTTTGCCTAGGGCACAAAGAGCTTTTTTTATTAATTCTCAAAAAATCACCAAAAATTTAAATGGTTATGTCGGAATCTCTGCTATCAt                                                  >  2:170201/5‑149 (MQ=255)
                                                                              tttATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTg                                                <  1:242152/149‑1 (MQ=255)
                                                                                 aTCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAg                                             <  2:232428/149‑1 (MQ=255)
                                                                                 aTCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAg                                             <  1:111964/149‑1 (MQ=255)
                                                                                   ccTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCt                                           >  2:72676/1‑149 (MQ=255)
                                                                                     tGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTaa                                         >  1:88106/1‑149 (MQ=255)
                                                                                        cGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTaaaaa                                      >  1:17398/1‑149 (MQ=255)
                                                                                        cGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTaaaaa                                      >  1:133948/1‑149 (MQ=255)
                                                                                            gCTAAAATTGACTTGAACGTGATGATCTATGATCTATCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATAAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAaacaa                                  <  2:21148/149‑1 (MQ=255)
                                                                                               aaaaTTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTa                               >  2:214219/1‑149 (MQ=255)
                                                                                                      aCTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTtgatg                        >  2:142908/1‑149 (MQ=255)
                                                                                                              gtaatgatctatgatctTACAAGCAATTTTTGCCTTGAGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCt                <  2:93795/146‑1 (MQ=255)
                                                                                                                   gatctatgatctTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGt           <  1:261834/149‑1 (MQ=255)
                                                                                                                    atctatgatctTTCAAGCACTTTTTGACTTGGGTAGAAAGTTCTTTTATAAAAAAAAAAAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTa          <  2:257395/149‑1 (MQ=255)
                                                                                                                    atctatgagctTTCAAGCACTTTTTGCCGTGGGTAGAAAGTGCTTTTTTTATAAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTa          <  2:62829/149‑1 (MQ=255)
                                                                                                                         taatcgTTCAAGCACTTTTTGCCGTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATc     <  2:148283/147‑1 (MQ=255)
                                                                                                                           atctTTCAAGCACTTTTTGCCTTGGTTAGAAAGTGCTTTTTTTATTTTTTTTTAAAAAAGCACCAACAATTTAAATGGCGGTGTCTTAATGTCTGCTATCATTTAAGCTAAAAAACAACTATTTTATGAAATTGCTTATGTACTATCaa   >  2:113442/1‑149 (MQ=255)
                                                                                                                            tctTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCaaa  >  1:253341/1‑149 (MQ=255)
                                                                                                                                                |                                                                                                                                
ACAATAAGTAATTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCGTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCAAA  >  USA300TCH1516_ALE/583977‑584249

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑