Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730110,6600TA21.9% 59.7 / 11.3 32I173I (ATT→ATA) USA300HOU_0109staphylococcal tandem lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (10/15);  new base A (4/3);  total (14/18)
Fisher's exact test for biased strand distribution p-value = 6.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.39e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTT  >  CP000730/110524‑110800
                                                                                                                                        |                                                                                                                                             
ttAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTACaa                                                                                                                                           >  2:213914/1‑140 (MQ=255)
            ataataAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAgg                                                                                                                               >  2:446185/1‑141 (MQ=255)
             aaaaaaaaACATTCCAACAAAAGAAATAAAAAAAAAAAAAAAAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGt                                                                                                                              <  2:56417/137‑1 (MQ=17)
                   aaTCATTCCAAAAAAAGAAATTAAAAATGAAAAAAAAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCG‑Ag                                                                                                                       <  2:245104/141‑1 (MQ=255)
                     tCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAAAGGTGCCG‑AGtt                                                                                                                     >  2:164792/1‑141 (MQ=255)
                       aTTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCG‑AGTTAt                                                                                                                   >  2:415214/1‑141 (MQ=255)
                              aaaaaGAAATTAAATAAGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTa                                                                                                            <  2:167665/140‑1 (MQ=255)
                                          aaGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTaa                                                                                                >  2:51355/1‑141 (MQ=255)
                                                  aaaaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAatgat                                                                                        <  2:155638/141‑1 (MQ=255)
                                                     aTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATgatgat                                                                                     <  2:407276/141‑1 (MQ=255)
                                                       aaaaaaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGATta                                                                                   >  2:70380/1‑141 (MQ=255)
                                                       aaaaaaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGATGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGAttt                                                                                   >  2:61874/1‑140 (MQ=255)
                                                         aaaaaGAAACCGAAAAGTTTAGGTTTTGTGTACAATATGGCGACTTTAAAAATTGAAACAGCTCGTAACCCGGCGATATTTCAGATAATCGAG‑GGTGGCGAAGACATTCGGCTAAATAACAATTAACTaaatgagaatata                                                                                 >  2:54710/1‑130 (MQ=255)
                                                             aGATATCGAAAACTTTAAGTTCTGTTTTCAATATGGCGACTTGAAAAATTTGAAAAAGTATAAAGACAGAGATATTTCTTATATCCCTGAGGTTCCG‑AGTTAGTCGGCTAAATATCAATTAACTAATGATGATTATAATGt                                                                             <  2:226477/141‑1 (MQ=14)
                                                             aGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGt                                                                             <  2:317178/141‑1 (MQ=255)
                                                                         gtttAAGTTCTTTGTTCAATATGGCGACTTGAAAAATTTGAAAAATTATAAAGACGGGGATATTTCATAGAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                 <  2:120990/140‑1 (MQ=255)
                                                                                  cTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgata                                                        <  2:216231/141‑1 (MQ=255)
                                                                                   tttGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAAGCAAAAgatat                                                       >  2:157716/1‑141 (MQ=255)
                                                                                    ttGTTCAATATGGCGACCTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatg                                                      <  2:196500/141‑1 (MQ=255)
                                                                                               ggCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATAGCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacg                                           <  1:10326/141‑1 (MQ=255)
                                                                                               ggCGACTTTAAAAAGTGGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacg                                           <  1:444/141‑1 (MQ=255)
                                                                                                 cGACTTAAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAg                                         <  2:107739/141‑1 (MQ=255)
                                                                                                        aaagatttaatgaaTTATAAAGATGGAGATATATCATCTAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAGGCAAAACATTTTATATACCGACGAGTAAAGCt                                  >  2:371286/13‑141 (MQ=11)
                                                                                                        aaagatttaatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCt                                  <  2:256627/129‑1 (MQ=11)
                                                                                                          agatttaatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTcc                                <  2:11000/131‑1 (MQ=14)
                                                                                                           gatttaatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATTTGATATACCGACGAGTAAAGCTCCa                               >  2:67261/10‑141 (MQ=11)
                                                                                                           aaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCa                               <  2:42132/141‑1 (MQ=255)
                                                                                                                      ttATAAAGACGTAGATATTTCATATAAACCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGtt                    <  2:19332/141‑1 (MQ=255)
                                                                                                                        tttgaGATGGAGATATATCATTTAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAGAGATATGATATACCGACGAGTGATGCTCCAAAGTTATTGTTaa                  <  2:458619/137‑1 (MQ=17)
                                                                                                                         taAAGAAGGAGATATATCATATAATCCAGAGATGCCA‑CGTTATTCGGCTCAATAACAATTAACTAATGATGATTATAATGTAAAGCAATTACGCAAAAGATATGATATACCGACGAGTAAAGCAACAAAGTTCTTGTaaaa                 >  2:137197/1‑141 (MQ=14)
                                                                                                                           aaGATGGAGATATATCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAg               >  2:408751/1‑141 (MQ=255)
                                                                                                                                   gaTATTTCATGTCATCGAGAGGTGCCG‑AGATATAAGGCGAAATATCAATTCGGCAACGAGCTGTAGAGAGGAAAACAATGACGGAAAAGATATGATATACCGACGAGTAAAGCTCGAAAGTTATTGTTAAAAGGTGCAggg       >  2:225798/1‑141 (MQ=255)
                                                                                                                                        ttCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATCTCAATTCACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGAAATACCGAAGAGAAAAGCTCCAACGGTATTGCTAAAAAGTTCAGGGGAtat  >  2:469506/1‑139 (MQ=17)
                                                                                                                                        |                                                                                                                                             
TTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCG‑AGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTT  >  CP000730/110524‑110800

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: ‑