Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 111,516 C→A 26.4% Q196K (CAA→AAA)  USA300HOU_0110 → possible staphylococcal tandem lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730111,5160CA26.4% 64.2 / 13.5 40Q196K (CAA→AAA) USA300HOU_0110possible staphylococcal tandem lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (14/15);  new base A (7/4);  total (21/19)
Fisher's exact test for biased strand distribution p-value = 4.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  CP000730/111377‑111651
                                                                                                                                           |                                                                                                                                       
tGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTc                                                                                                                                         <  1:205541/140‑1 (MQ=255)
       gTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTACCGAGTTATTCAGCTCAATATCa                                                                                                                                  >  1:261481/1‑140 (MQ=255)
        ttAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATAGATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCaa                                                                                                                                 >  1:182987/1‑140 (MQ=255)
          aaaGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAtt                                                                                                                               >  1:211503/1‑140 (MQ=255)
                 aaaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTAAATATCAATTAACTAat                                                                                                                        >  1:13742/1‑140 (MQ=255)
                  aaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatg                                                                                                                       >  2:242760/1‑140 (MQ=255)
                   aaCATAAAAAAAGAAATCGAAAAATTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGACTTATAAAGATGGAGATATATCATATAATCCAGCGGTGCCGAGTTATTTAGCTCAATATTAATTAACTAatga                                                                                                                      >  1:72191/1‑140 (MQ=21)
                    aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatgat                                                                                                                     >  1:212024/1‑140 (MQ=255)
                     cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgatg                                                                                                                    >  1:118599/1‑140 (MQ=255)
                        aaaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGAtt                                                                                                                 <  1:286750/140‑1 (MQ=255)
                         aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATta                                                                                                                >  1:129246/1‑140 (MQ=255)
                            aaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATaa                                                                                                             >  2:98546/1‑140 (MQ=255)
                             aaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAAt                                                                                                            <  1:162415/140‑1 (MQ=255)
                                    cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAAc                                                                                                     <  2:50454/140‑1 (MQ=255)
                                       taaCTTTTAGTTTTTTGCGAAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                  <  1:288968/139‑1 (MQ=255)
                                       aaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCTGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                  <  1:139443/140‑1 (MQ=255)
                                       aaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                  <  1:289059/140‑1 (MQ=255)
                                       aaaCTTTAAGTTGTTTGCGAAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                  <  1:206922/140‑1 (MQ=17)
                                          cTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAc                                                                                               >  1:206636/1‑140 (MQ=255)
                                          cTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTACTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAc                                                                                               <  2:205680/140‑1 (MQ=255)
                                            ttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                             <  2:9414/140‑2 (MQ=255)
                                             tAAGTTTTTTGCGCAATATAGCAATTTTAAAGCTTTCATGAATGATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTa                                                                                            <  1:59384/140‑1 (MQ=255)
                                             tAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTa                                                                                            <  2:250827/140‑1 (MQ=255)
                                               aGTTTATTGTGCAATATCGCAATTTTAAAGAGTTAATGAAATATAAAGATGGAGATATATCATATAGTCCAGAGGTGCCGAGTTATTCGGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaa                                                                                          >  1:235632/1‑140 (MQ=17)
                                                gTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaaaa                                                                                         <  1:254574/140‑1 (MQ=255)
                                                       gcgcAATATAGCAATTTTAAAGCTATACTAGTTGATAAAGATGGAGATATATCATATAATCCAGAGTTGCCGAGTTATTCAGCTCAATATCAATTACCTAATGCTGATTATAATGTAAAACAATTACGTAAAAGAAATGa                                                                                  >  1:76510/1‑140 (MQ=17)
                                                       gcgcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGa                                                                                  <  2:312266/140‑1 (MQ=255)
                                                              ataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATCTAATCTCACTAAAAGGTGACGAAAGCTACTGCTAAATATCAATTAACTACTGATAATTAGAATGTGAAACAATTACGCAAAAGATATGATATAccg                                                                           >  1:75497/1‑139 (MQ=9)
                                                                         aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAGCAAATAAAgc                                                                <  1:234543/140‑1 (MQ=255)
                                                                                         gtaAAGAGTGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGttcttg                                                <  1:229947/139‑1 (MQ=255)
                                                                                            aaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGaaa                                             >  2:196398/1‑140 (MQ=255)
                                                                                                        tatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACACATAAAGCGCCGAAGCTGTTGTTGAAGGGAACAGGGaaa                                 >  2:76053/1‑139 (MQ=255)
                                                                                                         atCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAtt                                <  2:162485/140‑1 (MQ=255)
                                                                                                          tCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTATAAGCTTTACGTACAAGATACTACAGACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt                               <  1:315454/140‑1 (MQ=17)
                                                                                                             tataATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaaa                            >  2:35810/1‑140 (MQ=255)
                                                                                                                     agatGTGCCGAGTTATTTAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACAGACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAATGTACAGCGAATTTAAAAGGTtcat                    <  2:72191/140‑1 (MQ=17)
                                                                                                                         gTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATAATAATGTAAAACAATTACGCAAAAGATATGCTATAACAAAAAATAAAGCGCCGAAGCTATTGTTAAAAAGTACAGAGAATTTAAAAGGTTCATCAGt                >  2:104346/1‑140 (MQ=11)
                                                                                                                          tGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGtt               >  2:172516/1‑140 (MQ=255)
                                                                                                                            ccGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTgg             >  2:182099/1‑140 (MQ=255)
                                                                                                                                     tCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaa    <  1:196398/140‑1 (MQ=255)
                                                                                                                                       aGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGACAGGTACAGGGAATTTAAAAGGTTCCTCAGTTCGACATgaaaaaa  >  1:319764/1‑140 (MQ=17)
                                                                                                                                           |                                                                                                                                       
TGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  CP000730/111377‑111651

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: ‑