Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 110,660 T→A 20.3% I173I (ATT→ATA)  USA300HOU_0109 → staphylococcal tandem lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730110,6600TA20.3% 82.4 / 16.8 39I173I (ATT→ATA) USA300HOU_0109staphylococcal tandem lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (8/23);  new base A (5/3);  total (13/26)
Fisher's exact test for biased strand distribution p-value = 8.96e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.49e-01

TAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAAT  >  CP000730/110525‑110798
                                                                                                                                       |                                                                                                                                          
tAAAACGGTCGATAATAAAATCATTCCAAAAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCat                                                                                                                                        <  1:50430/140‑1 (MQ=255)
  aaaTGTTCGATAATAAAAACAGTACAACAAAAGAAATGAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTGTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCatat                                                                                                                                      <  1:21574/140‑1 (MQ=17)
  aaaTGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAATAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCatat                                                                                                                                      <  1:127216/140‑1 (MQ=255)
               taaAATCATTCCAACAAAAGAAATTAAAGATTAAAAAATAAAAAAAGAAATCTAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGc                                                                                                                         <  1:79705/140‑1 (MQ=255)
                  aaTCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGa                                                                                                                      <  2:85610/140‑1 (MQ=255)
                    tCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGATTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGt                                                                                                                    <  1:180117/140‑1 (MQ=255)
                          caacaaAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATACAGAGGTGCCGAGTTATTCg                                                                                                              >  2:76317/1‑140 (MQ=255)
                              aaaaGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTa                                                                                                          <  1:166489/140‑1 (MQ=255)
                                          aGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTaa                                                                                              >  1:266777/1‑140 (MQ=255)
                                          aGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTaa                                                                                              <  1:136603/140‑1 (MQ=255)
                                            aTGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                            <  1:46506/140‑1 (MQ=255)
                                                     tAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATgatgat                                                                                   <  1:191782/140‑1 (MQ=255)
                                                               aaTCGAAAGCTTGAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaa                                                                         <  2:85319/140‑1 (MQ=255)
                                                                aTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaaa                                                                        >  1:223588/1‑140 (MQ=255)
                                                                aTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTAGGATAAATATCAATTAACTAATGATGATTATAATGTaaa                                                                        >  1:78964/1‑140 (MQ=255)
                                                                aTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTCATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaaa                                                                        >  2:149546/1‑140 (MQ=255)
                                                                     aaacgggaaGTTCTTTGTTCAATATGGCGACATTAAAAATTTGAAAGATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGACGAGTTATTCGGCTAAATATCAATTAACTGATGATGATGATAATGTAAAACAAt                                                                   >  2:251946/8‑140 (MQ=17)
                                                                       aCTTTAAGTGCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                 <  2:229416/140‑1 (MQ=255)
                                                                        cTTTAATTTTTTTTTTTAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTCCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAAGGATGATTATAATGTAAAACAATTAc                                                                <  1:32335/140‑1 (MQ=17)
                                                                           tAAGTTCCTTGTTCAATATGGCGACTTTAAAAATTTGAAAAAGTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCa                                                             <  2:200253/140‑1 (MQ=255)
                                                                             aGTTCTTTGTTCAATATCGTGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaa                                                           <  1:165566/140‑1 (MQ=255)
                                                                             aGTGCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaa                                                           >  2:670/1‑140 (MQ=255)
                                                                                 cTTTGTTCAATATGGCTAAGTTAAAAATTTGAAAAATTATAAAGACGGAGATAATTCATAAAATGCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgat                                                       <  1:17448/140‑1 (MQ=17)
                                                                                    gggtcgatttGGCTACTTTAAAAATTTGATAAATTATATATACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATTATTATAATGTAAAACAATTACGCAAAAgatatg                                                    <  2:137092/131‑1 (MQ=17)
                                                                                                 gACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGCGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAg                                       <  2:237246/140‑1 (MQ=255)
                                                                                                        aagatttaatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAATAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGAAATACCGACGAGAAAAGCt                                >  1:130896/12‑140 (MQ=11)
                                                                                                        aaaaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATAAGATATACCGACGAGTAAAGCt                                >  1:201318/1‑140 (MQ=255)
                                                                                                         agatttaatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTc                               <  2:142995/130‑1 (MQ=14)
                                                                                                            tttaatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGAATATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCaa                            >  1:172859/8‑140 (MQ=14)
                                                                                                              tGAAAAATTATAAAGACTGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAg                          <  1:17414/140‑1 (MQ=255)
                                                                                                              tGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATAGCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAg                          <  1:59359/140‑1 (MQ=255)
                                                                                                                     ttATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGt                   >  1:148638/1‑140 (MQ=255)
                                                                                                                     ttATAAAGAGGGAGATATATCATAGAAGCCAGAGGTGCCGAGTTATTCGGCTAAAGATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACGGACGAGTAAAGGTCCAAAGTTATTGt                   <  2:146434/140‑1 (MQ=17)
                                                                                                                      tataAAGATGGAGATATATCATATAATCCAGAAATGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACGGACGAGTAAAGCTCCAAAGATATTGtt                  >  2:60244/1‑140 (MQ=17)
                                                                                                                       ataAAGATGGAGATATATCATATAATCCATGTGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCCAAGTTATTGTTa                 >  2:161058/1‑140 (MQ=17)
                                                                                                                         aaaGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaaa               <  1:217423/140‑1 (MQ=255)
                                                                                                                            gatggAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAgg            <  1:11424/137‑1 (MQ=255)
                                                                                                                                   atatTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAggg     <  1:171829/140‑1 (MQ=255)
                                                                                                                                     atTGCATAGAATCCAGAGGTGCCGAGTTATCCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGaa   <  2:180962/140‑1 (MQ=255)
                                                                                                                                      tttCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAAt  <  2:266777/140‑1 (MQ=255)
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TAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAAT  >  CP000730/110525‑110798

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: ‑