Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,679,708 G→A 64.6% W64* (TGG→TGA USA300HOU_2536 → possible secretory antigen

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,679,7080GA64.6% 15.6 / 11.8 22W64* (TGG→TGAUSA300HOU_2536possible secretory antigen
Reads supporting (aligned to +/- strand):  ref base G (3/5);  new base A (8/6);  total (11/11)
Fisher's exact test for biased strand distribution p-value = 6.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTT  >  CP000730/2679584‑2679825
                                                                                                                            |                                                                                                                      
cTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAAtt                                                                                                        <  2:102308/141‑1 (MQ=255)
      aaTCCGTCGAATAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTAtt                                                                                                  <  2:79970/141‑1 (MQ=255)
             cGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGATATTACAATGc                                                                                           >  1:74708/1‑141 (MQ=255)
              gAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACaaggga                                                                                          >  1:73608/1‑137 (MQ=255)
                      gCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATc                                                                                  >  1:167682/1‑141 (MQ=255)
                        attcaTCGCATGCCGCAGTTAATTGTTAGAGTAAAGACCAAATCACATGGTGTGTATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCaa                                                                                <  1:106245/137‑1 (MQ=255)
                            aTCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGGTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAAtacaagta                                                                            >  1:50197/1‑134 (MQ=255)
                               gCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGc                                                                         <  2:47635/141‑1 (MQ=255)
                                 aTGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTTGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGGATTACAATGCAGGTAAATGAAAATATgaga                                                                       >  2:105779/1‑141 (MQ=255)
                                               tattatAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAGAAATTGGTATTACAATGCACGTAACTAAAAATATGGCACTGGCCGTACACCa                                                        >  2:38650/1‑141 (MQ=255)
                                                             ccAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGGCGGTAAACCTGTTGCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGt                                          <  2:4522/141‑1 (MQ=255)
                                                             ccAATGTACAGGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATAGGGCAATGCTAAAAATTAGTCGTACAATGCACGTAAATCAAAATATGAGACTGGTAGTCACACAAGAAACGTTGcagg                                          >  2:37007/1‑138 (MQ=255)
                                                                aTGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCGGTCAt                                       >  2:145611/1‑141 (MQ=255)
                                                                     cATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAAt                                  <  1:165430/141‑1 (MQ=255)
                                                                     cATGGTGGGCAATTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAAt                                  <  2:158892/141‑1 (MQ=255)
                                                                              aaTTTCAACGTGGCGCAAAAGTCGGTCACTCTTTTGCGAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGGAAATCAAAAGATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAg                         <  1:244051/140‑1 (MQ=255)
                                                                                  tAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGata                     >  2:177111/1‑141 (MQ=255)
                                                                                     aCGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGAtattt                  >  1:94667/1‑140 (MQ=255)
                                                                                               caAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTc        <  1:197942/141‑1 (MQ=255)
                                                                                               caAGTCGGTAAACCTGTTTCTAAGAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTc        <  2:229046/141‑1 (MQ=255)
                                                                                               caAGGCGGTAAACCGGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTc        <  2:229054/141‑1 (MQ=255)
                                                                                                     ggTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTAGccgat  >  1:130964/1‑137 (MQ=255)
                                                                                                                            |                                                                                                                      
CTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTT  >  CP000730/2679584‑2679825

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: