Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE110,6600TA30.4% 24.7 / 13.6 23I173I (ATT→ATA) USA300HOU_RS00515putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (5/11);  new base A (3/4);  total (8/15)
Fisher's exact test for biased strand distribution p-value = 6.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.10e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGA  >  USA300TCH1516_ALE/110522‑110796
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ggTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATAttt                                                                                                                                         >  2:282444/1‑140 (MQ=255)
     aaaTAGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCatat                                                                                                                                    <  2:236767/140‑1 (MQ=255)
        tGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAGGAAGGCGACGTTAAAAATTTGAAAACTTATAAAGACGGAGATATTTCATATAAt                                                                                                                                 >  1:12096/1‑140 (MQ=17)
                    aaaTCATTCCAACAAAAGAAATTAAAAATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCg                                                                                                                     <  1:275249/140‑1 (MQ=255)
                                 aaaaGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAACCTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTa                                                                                                        <  1:314688/140‑1 (MQ=255)
                                 aaaaGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTa                                                                                                        <  1:88716/140‑1 (MQ=255)
                                     gAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                    <  1:282444/140‑1 (MQ=255)
                                        aTTAAAGATGAAAAAATAAAAAAATTAATCGAAAATTTTAAGTTCTTTGTTTAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCa                                                                                                 <  1:205229/140‑1 (MQ=255)
                                           aaaGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGACATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAAtt                                                                                              >  1:227305/1‑140 (MQ=255)
                                                  aaaaaaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATAAATTAACTAat                                                                                       >  1:1004/1‑140 (MQ=255)
                                                           aaaaaaaaACAGAAAACATTAAGTTCATAGTTCAATATTGGTACTTTAAAAATTTTAAAAATTATAAAGTCGGAGATATTACATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtat                                                                              <  2:162911/140‑1 (MQ=14)
                                                                           cTTTAAGTTTTTTGTTCAAGATGGCGTCTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAc                                                              <  2:38595/140‑1 (MQ=255)
                                                                                    cgttGTTCAATAAGGCCACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgat                                                     <  2:255846/138‑1 (MQ=255)
                                                                                                       tttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTaa                                  <  1:284347/140‑1 (MQ=11)
                                                                                                         tAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAg                                <  2:227305/140‑1 (MQ=255)
                                                                                                                     taaTTATAAATATGGAGAGATATGATATAATCGAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATTTACCTACGAGTAAAGCTCCAAAGTTAt                    <  2:102750/139‑1 (MQ=17)
                                                                                                                        ttATAAAGATGGATATATATTATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGt                 <  2:240040/140‑1 (MQ=255)
                                                                                                                           taAAGAGTGAGAAATATCATATAAGTCAGAGGTGCCGAGTTATTCGGGTAAATATAAATTAACTAATGATGATTATAGTGTAAAACAATTACTCAAAAGATATGATATCCCGACGAGTAAAGCTCCAAAGTTATTGTTaa              <  2:118739/140‑1 (MQ=18)
                                                                                                                            aaaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAATTATTGTTaaa             >  2:292660/1‑140 (MQ=255)
                                                                                                                               gatggAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAACGACGAATAAAGCTCCAAATTTATTGTTAAAAga          >  1:190994/4‑139 (MQ=17)
                                                                                                                                aCGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACACAAAAGATATAATATACCGACGAGTAAAGCTCCAAAGATATTGTTAAAAGGt         >  2:175223/1‑140 (MQ=255)
                                                                                                                                 cGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGtt        <  2:12096/140‑1 (MQ=255)
                                                                                                                                   gagaTATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACAGACGAGTAAAGCTCCAAAGTTATTTTTAAAATGTTCa      >  1:43355/1‑140 (MQ=255)
                                                                                                                                       tatTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTCCGACAAAGATATGATATACTGCTGAGCAAAGCTCCAAAGTTATTGTTAAAACGTTCAGGGa  >  2:301446/1‑140 (MQ=18)
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GGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGA  >  USA300TCH1516_ALE/110522‑110796

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: ‑