Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE110,6600TA24.0% 42.9 / 11.0 25I173I (ATT→ATA) USA300HOU_RS00515putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (9/10);  new base A (6/0);  total (15/10)
Fisher's exact test for biased strand distribution p-value = 5.08e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.04e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAA  >  USA300TCH1516_ALE/110531‑110797
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ggTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAAACGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATc                                                                                                                                 >  2:103433/1‑140 (MQ=255)
     ataaaaAAATCAGTACAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCagag                                                                                                                            <  2:123333/140‑1 (MQ=255)
      taataaAATCATTCCAACAAAACAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGATCTTTGTTCAATATAGCGACTTTAAAAATTTCAAAAATTATAAAGACGGAAAAATATCATATAAACCAAAgg                                                                                                                           >  2:64213/1‑140 (MQ=17)
          aaaaTCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAACACGGAGATATTTCATATAATCCAGCGGTGcg                                                                                                                       >  1:55424/1‑139 (MQ=255)
          aaaaTAATTACAACAATTGAAAATAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGcc                                                                                                                       <  2:77543/140‑1 (MQ=17)
              taaTTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGt                                                                                                                   <  2:204746/138‑1 (MQ=255)
              tCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGt                                                                                                                   >  2:247948/1‑140 (MQ=255)
                           aGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACATTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAat                                                                                                      <  1:104408/140‑1 (MQ=255)
                                 tAAAGAGGAAAGAAGAAAAAAAGAAATCGAAAACTTTAAGTTGTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAAt                                                                                                <  1:93873/140‑1 (MQ=255)
                                                      aGAATTCTAAAATTTTAAGTTTTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATg                                                                           <  2:27635/140‑1 (MQ=255)
                                                        aaaTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTa                                                                         >  1:142383/1‑140 (MQ=255)
                                                                    ttAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACTGTGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGc                                                             >  1:50223/1‑140 (MQ=255)
                                                                    ttAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGc                                                             >  1:62379/1‑140 (MQ=255)
                                                                                       tGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcga                                          <  1:130501/140‑1 (MQ=255)
                                                                                                  aaaaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCt                               <  1:247948/140‑1 (MQ=255)
                                                                                                       ttGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGATTAAAGCTACaaa                          >  2:168519/1‑140 (MQ=255)
                                                                                                       ttGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCaaa                          >  1:227997/1‑140 (MQ=255)
                                                                                                       ttGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACAGACGAGTACAGCTCCaac                          >  2:168938/1‑139 (MQ=255)
                                                                                                        taatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAAATGTGTGAGACCGACGAGTAAAGCTCCAAAg                         >  2:105079/6‑140 (MQ=14)
                                                                                                          atgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGtt                       >  1:133175/4‑140 (MQ=255)
                                                                                                                     agatggAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAg            >  2:193673/5‑140 (MQ=255)
                                                                                                                           agaTATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAg      >  1:249129/1‑140 (MQ=255)
                                                                                                                            gaTATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAACGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAgg     >  1:160321/1‑140 (MQ=255)
                                                                                                                             atatTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAggg    <  2:62379/140‑1 (MQ=255)
                                                                                                                               atTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGaa  <  2:50223/140‑1 (MQ=255)
                                                                                                                                 |                                                                                                                                         
GGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAA  >  USA300TCH1516_ALE/110531‑110797

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: ‑