Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730110,6600TA24.5% 90.8 / 33.0 49I173I (ATT→ATA) USA300HOU_0109staphylococcal tandem lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (10/27);  new base A (5/7);  total (15/34)
Fisher's exact test for biased strand distribution p-value = 4.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.09e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAA  >  CP000730/110520‑110797
                                                                                                                                            |                                                                                                                                         
ccGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATAtt                                                                                                                                           >  1:240759/1‑141 (MQ=255)
 cGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAAATAAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATAttt                                                                                                                                          <  2:57184/141‑1 (MQ=255)
      aaaaTGGTCGATAATAAAATCATACCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCatat                                                                                                                                     <  2:104939/141‑1 (MQ=255)
          tGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGAGTAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTAAATATGGCAACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATc                                                                                                                                 >  2:355625/1‑141 (MQ=255)
            atCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGATCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATcga                                                                                                                               >  2:277518/2‑139 (MQ=255)
             tCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCag                                                                                                                              <  1:292879/141‑1 (MQ=255)
                ataataAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAgg                                                                                                                           >  1:245951/1‑141 (MQ=255)
                ataataAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAgg                                                                                                                           <  1:179444/141‑1 (MQ=255)
                      aaaTCATTCCAACAAAAGAAATT‑AAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAAATTAAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAg                                                                                                                    <  2:155890/141‑1 (MQ=255)
                            ttCCAACAAAAGAAACTAAAGATGAAAAAATAAAAAACGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGaataact                                                                                                               <  1:352328/141‑7 (MQ=255)
                             tCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAAACGAAGATATTTCATATAATCCAAAGGTGCCGAGTTATTc                                                                                                              >  2:391677/1‑141 (MQ=255)
                              ccAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCg                                                                                                             <  2:268879/141‑1 (MQ=255)
                              ccAACAAAAGAAATTAAAGATGAAAAAAAAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCg                                                                                                             <  2:34944/141‑1 (MQ=255)
                               caacaaAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCgg                                                                                                            <  1:386243/141‑1 (MQ=255)
                                         aaTTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCa                                                                                                  <  1:210587/141‑1 (MQ=255)
                                                      aaaaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgat                                                                                     <  2:342370/141‑1 (MQ=255)
                                                       aaaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgatg                                                                                    >  1:141928/1‑141 (MQ=255)
                                                        aaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAAtgatga                                                                                   <  1:164623/141‑1 (MQ=255)
                                                         aTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATgatgat                                                                                  <  1:12705/141‑1 (MQ=255)
                                                                aaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATg                                                                           <  2:198577/141‑1 (MQ=255)
                                                                  gAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTa                                                                         <  2:215959/141‑1 (MQ=255)
                                                                   gaatcgaggaggttAAGTTGTTGGTTGAATATGGCGAGTTTAAAAGTTTGAAAAATTATAAAGAGGGAGGTATTTCATATGATGCAGAGGTGCCGAGTTATTCGGGTAAATATCAATTAACTCTTGATGATTATGATGTaa                                                                        <  2:332226/129‑1 (MQ=17)
                                                                    aaTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTACCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaaa                                                                       >  2:382454/1‑141 (MQ=255)
                                                                        gAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACaa                                                                   <  1:224337/141‑1 (MQ=255)
                                                                              tttAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTGTAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGGTTATAATGTAAAACAATTACGc                                                             >  1:370846/1‑141 (MQ=255)
                                                                                      cTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgata                                                     <  2:272476/141‑1 (MQ=255)
                                                                                      cTTTGTTCAATATGGCGAATTTTCAACGTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgata                                                     >  2:222674/1‑141 (MQ=17)
                                                                                         tggtCAATATGGCGACTTTAAAAATTTGAAAAAGTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatga                                                  <  2:247496/138‑1 (MQ=255)
                                                                                                        cTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAATATATGATATACCGACGAGTaa                                   <  1:439865/141‑1 (MQ=255)
                                                                                                        cTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTaa                                   <  1:381556/141‑1 (MQ=255)
                                                                                                             aagatttaatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTc                              >  2:45673/12‑141 (MQ=11)
                                                                                                             aaaaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTc                              >  2:316612/1‑141 (MQ=255)
                                                                                                             aaaaTTTGAAAAATTATAAAGACGGAGATATTGCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTc                              <  1:165903/141‑1 (MQ=255)
                                                                                                              aaaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTcc                             <  1:277518/141‑1 (MQ=255)
                                                                                                                 tttaatgaaTTATAAAGATGGGGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCaaa                          <  1:312291/134‑1 (MQ=14)
                                                                                                                   taatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGt                        <  1:212032/136‑1 (MQ=255)
                                                                                                                    gAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGtt                       >  1:340992/1‑141 (MQ=255)
                                                                                                                       gaaTTATAAAGTTGTATATATAACATATAATCCAGAGTTGGCGAGTTATTCGAGTAAATATCAATTAACTAATGATGATTATAATGTATAACATTGAAGAAAAAGATATGATATACCGACGAGAAAAGCCACAAACATAtt                    >  2:12464/2‑141 (MQ=9)
                                                                                                                       gaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTAtt                    <  1:164728/140‑1 (MQ=255)
                                                                                                                        aaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTg                   >  1:171218/1‑141 (MQ=255)
                                                                                                                          ttATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGtt                 >  2:206489/1‑141 (MQ=255)
                                                                                                                           gataAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTa                <  1:1667/140‑1 (MQ=255)
                                                                                                                            ataAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaa               <  1:323153/141‑1 (MQ=255)
                                                                                                                             taAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaaa              >  1:438802/1‑141 (MQ=255)
                                                                                                                                  atggAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGtt         <  2:437207/139‑1 (MQ=255)
                                                                                                                                  aCGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGtt         <  1:4862/141‑1 (MQ=255)
                                                                                                                                      agaTATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAgg     <  1:257329/141‑1 (MQ=255)
                                                                                                                                       gaTATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAggg    <  1:398010/141‑1 (MQ=255)
                                                                                                                                       gaTATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAggg    <  1:428474/141‑1 (MQ=255)
                                                                                                                                       gaTATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAggg    <  2:52672/141‑1 (MQ=255)
                                                                                                                                         tatTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGAAATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGaa  <  2:274486/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                         
CCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAA  >  CP000730/110520‑110797

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑