Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,845,6340GA20.7% 59.0 / 11.1 29F620F (TTC→TTT) isdHIron‑regulated surface determinant protein H
Reads supporting (aligned to +/- strand):  ref base G (7/16);  new base A (3/3);  total (10/19)
Fisher's exact test for biased strand distribution p-value = 6.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.51e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TGTGATGTATCATCATCTTTTGTATTGATATCCTGATTTATAATTCTGACATGATATTGACCTTCATAACCAATGTTTGCCACAACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTCCAGTAACTGTCATCCTTTGTTTTCATCACTACATATTTTTGACCATTTAAAGT  >  USA300TCH1516_ALE/1845503‑1845765
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tgtgATGTATCATCATCTTTTGTATTGATATCCTGATTTATAATTCTGACATGATATTGACCTTCATAACCAATGTTTGCCACAACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGAAAAATCAGc                                                                                                                            >  2:201720/1‑141 (MQ=255)
tgtgATGTATCATCATCTTTTGTATTGATATCCTGATTTATAATTCTGACATGATATTGACCTTCATAACCAATGTTTGCCACAACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGAAAAATCAGc                                                                                                                            >  2:171094/1‑141 (MQ=255)
tgtgATGTATCATCATCTTTTGTATTGATATCCTGATTTATAATTCTGACATGATATTGACCTTCATAACCAATGTTTGCCACAACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGAAAAATCAGc                                                                                                                            >  2:169837/1‑141 (MQ=255)
     tGTATCATCATCTTTTGTATTGATATCCTGATTTATAATTCTGACATGATATTGACCTTCATAACCAATGTTTGCCACAACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCt                                                                                                                       >  1:105247/1‑141 (MQ=255)
      gTATCATCATCTTTTGTATTGATATCCTGATTTATAATTCTGACATGATATTGACCTTCATAACCAATGTTTGCCACAACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTa                                                                                                                      <  2:118493/141‑1 (MQ=255)
                                cTGATTTATAATTCTGACATGATATTGACCTTCATAACCAATGTTTGCCACAACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAAc                                                                                            >  2:143717/1‑141 (MQ=255)
                                 tGATTTATAATTCTGACATGATATTGACCTTCATAACCAATGTTTGCCACAACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACa                                                                                           <  2:98951/141‑1 (MQ=255)
                                              tGACATGATATTGACCTTCATAACCAATGTTTGCCACAACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGtt                                                                              <  1:29473/141‑1 (MQ=255)
                                              tGACATGATATTGACCTTCATAACCAATGTTTGATACAACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGtt                                                                              <  1:161942/141‑1 (MQ=255)
                                                                   aaCCAATGTTTGCCACAACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTGGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCtt                                                         <  2:14069/141‑1 (MQ=255)
                                                                   aaCCAATGTTTGCCACAACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCtt                                                         <  2:24615/141‑1 (MQ=255)
                                                                      cAATGTTTGCCACAACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTcc                                                      >  1:212017/1‑141 (MQ=255)
                                                                         tGTTTGCCACAACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTCCAGt                                                   <  2:105247/141‑1 (MQ=255)
                                                                              gCCACAACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTCCAGTAACTg                                              >  2:81568/1‑141 (MQ=255)
                                                                              gCCACAACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTCCAGTAACTg                                              <  2:200483/141‑1 (MQ=255)
                                                                                 acaACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTCCAGTAACTGTCa                                           <  1:109401/141‑1 (MQ=255)
                                                                                  caACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAATTCTTTCCAGTAACTGTCAt                                          <  1:8749/141‑1 (MQ=255)
                                                                                  caACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTCCAGTAACTGTCAt                                          <  2:31559/141‑1 (MQ=255)
                                                                                                aTCGCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTCCAGTAACTGTCATCCTTTGTTTtcatc                            <  1:65748/141‑1 (MQ=255)
                                                                                                   gCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTCCAGTAACTGTCATCCTTTGTTTTCATCACt                         <  2:161413/141‑1 (MQ=255)
                                                                                                    cATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTCCAGTAACTGTCATCCTTTGTTTTCATCACTa                        <  1:149761/141‑1 (MQ=255)
                                                                                                    cATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTCCAGTAACTGTCATCCTTTGTTTTCATCACTa                        <  1:149743/141‑1 (MQ=255)
                                                                                                     aTTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTCCAGTAACTGTCATCCTTTGTTTTCATCACTAc                       >  2:29565/1‑141 (MQ=255)
                                                                                                      ttGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTCCAGTAACTGTCATCCTTTGTTTTCATCACTACa                      <  2:104797/141‑1 (MQ=255)
                                                                                                                       aGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTATGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTCCAGTAACTGTCATCCTTTGTTTTCATCACTACATATTTTTGACCATTTaa     >  2:120792/1‑141 (MQ=255)
                                                                                                                       aGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTCCAGTAACTGTCATCCTTTGTTTTCATCACTACATATTTTTGACCATTTaa     >  2:37828/1‑141 (MQ=255)
                                                                                                                          tatataTGGAAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTCCAGTAACTGTCATCCTTTGTTTTCATCACTACATATTTTTGACCATTTAAAGt  <  1:169837/141‑1 (MQ=255)
                                                                                                                          tatataTGGAAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTCCAGTAACTGTCATCCTTTGTTTTCATCACTACATATTTTTGACCATTTAAAGt  <  1:171094/141‑1 (MQ=255)
                                                                                                                          tatataTGGAAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTCCAGTAACTGTCATCCTTTGTTTTCATCACTACATATTTTTGACCATTTAAAGt  <  1:201720/141‑1 (MQ=255)
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TGTGATGTATCATCATCTTTTGTATTGATATCCTGATTTATAATTCTGACATGATATTGACCTTCATAACCAATGTTTGCCACAACGACTTTAACAATCGCATTGTAAACTGCTTTGTCAGGTATATATGGGAAAATCAGCGTTCTAGAATTATTTTTAGGATCTTTAGAAACAGTAGTGACACGTTTACCTTCTACAATTAAATCTTTCCAGTAACTGTCATCCTTTGTTTTCATCACTACATATTTTTGACCATTTAAAGT  >  USA300TCH1516_ALE/1845503‑1845765

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑