Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,864,675 G→T 13.7% intergenic (+439/+1110) USA300HOU_2709 → / ← USA300HOU_2710 hypothetical protein/hypothetical membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,864,6750GT13.7% 73.5 / 2.7 29intergenic (+439/+1110)USA300HOU_2709/USA300HOU_2710hypothetical protein/hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base G (17/8);  new base T (2/2);  total (19/10)
Fisher's exact test for biased strand distribution p-value = 5.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

ATTGTAGTGTATTTGTTTAGAATATCCTCTTTTTTAGTTATGAATTTGTTACAAATATTAAGTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGAAATCACTGAAGGTCAACGTGGAGACCAAGCAG  >  CP000730/2864541‑2864809
                                                                                                                                      |                                                                                                                                      
aTTGTAGTGTATTTGTTTAGAATATCCTCTTTTTTAGTTATGAATTTGTTACAAATATTAAGTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCa                                                                                                                                   >  1:240073/1‑140 (MQ=255)
  tGTAGTGTATTTGTTTAGAATATCCTTTTTTTTAGTTATGAATTTGTTACAAATATTAAGTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGTTTTCATc                                                                                                                                 <  2:75760/140‑1 (MQ=255)
              gcttAGAATATCCTCTTTTTTAGTTATGAATTTGTTACAAATATTCAGTGCAAAATCACACGGAGGTTTTCTATATGAATAACTGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAAt                                                                                                                     <  2:324093/138‑1 (MQ=255)
              gTTTAGAATATCCTCTTTTTTAGTTATGAATTTGTTACAAATATTAAGTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAAt                                                                                                                     <  1:220078/140‑1 (MQ=255)
                                   aatagtGAATTTGTTAAAAATATTAATTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACAt                                                                                                <  1:132042/135‑1 (MQ=255)
                                    gTTATGAATTTGTTACAAATATTAAGTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACAtt                                                                                               >  2:237553/1‑140 (MQ=255)
                                              tGTTACAAATATTAAGTGCAAAAGCAGACGGAGGTTTTCTATATGAATAACGGTAGAGTAAGATGGTTTAACGCAGAAAAAGGAATTGGAATAATCGAACAAGAAAATGGCGGAAAAGTATTCGTACAGTTCTCAGGGAt                                                                                     >  2:226644/1‑140 (MQ=255)
                                                   cAAATATTAAGTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATAGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTa                                                                                >  1:2996/1‑140 (MQ=255)
                                                     aaTATTAAGTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGc                                                                              >  1:101798/1‑140 (MQ=255)
                                                            aGTGCAAAAGCACACGGAGTTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCt                                                                       <  2:240073/140‑1 (MQ=255)
                                                            aGTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCt                                                                       <  2:47863/140‑1 (MQ=255)
                                                             gTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCACTAGCGATGGCTa                                                                      >  1:341115/1‑140 (MQ=255)
                                                                     gCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACtt                                                              <  2:113332/140‑1 (MQ=255)
                                                                      cacaCGGAGGTTTTCTATATGAATACGGGCACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACttt                                                             >  1:353700/1‑140 (MQ=255)
                                                                          cGGAGGTTTTCTATATGCCGTCCGAGACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGTTTTCATCGAACAAGAAAATGGCGGAAACGTATTCGTACATTTCCCAGGTATCGCTAGCGATGGCTACAAAACTTTagaa                                                         >  2:164140/1‑140 (MQ=255)
                                                                          cGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTATCAGGTATCGCTAGCGATGGCTACAAAACTTTagaa                                                         >  2:282131/1‑140 (MQ=255)
                                                                          cGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTagaag                                                        >  2:318282/1‑140 (MQ=255)
                                                                            gAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAAACGTATTCGTACATTTCTCAGGTATCACTAGCGAAGGCTACAAAAATTTaaaaga                                                       >  1:137448/1‑140 (MQ=25)
                                                                              ggTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGAAGTATTCGTACATTTCTCAGGTATCGATAGCAATGGCTACAAAACTTTAGaagaag                                                     >  1:166943/1‑140 (MQ=255)
                                                                                                   tACAGTAAAATGGTTTAACGCAGAAAAATGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGaaa                                <  2:130249/140‑1 (MQ=255)
                                                                                                   tACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGTTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGaaa                                >  2:179525/1‑140 (MQ=255)
                                                                                                      aGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAGGAAGGTCAAAAATTTGTTTTCGAAAtaa                             >  2:101250/1‑138 (MQ=25)
                                                                                                       gTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGGCGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGAAATCAc                            >  1:215006/1‑140 (MQ=255)
                                                                                                              ggTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGAAATCACTGAAGGt                     <  1:307048/140‑1 (MQ=255)
                                                                                                                 ttAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGAAATCAATGAAGGTCaa                  >  1:30205/1‑140 (MQ=255)
                                                                                                                  tAACTCATAAAAAGGTTTTGTTTTCATCGAACAAGAAAATTGCTTATACTTATTCTTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGAAATCACTGAAGGTCAAc                 <  1:276291/140‑1 (MQ=255)
                                                                                                                   aaCGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGAAATCACTGAAGGTCAACg                >  2:275777/1‑140 (MQ=255)
                                                                                                                            aaaGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCCAAAAGTTACTTTCGAAATCACTGAAGGTCACCGTGGAGACCa       >  2:106834/1‑140 (MQ=255)
                                                                                                                                 ttttGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGAAATCACTGAAGGTCAACGTGGAGAACAAgacg  >  2:39307/1‑137 (MQ=255)
                                                                                                                                      |                                                                                                                                      
ATTGTAGTGTATTTGTTTAGAATATCCTCTTTTTTAGTTATGAATTTGTTACAAATATTAAGTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGAAATCACTGAAGGTCAACGTGGAGACCAAGCAG  >  CP000730/2864541‑2864809

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: