Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,766,3910CA20.0% 140.5 / 30.4 50Q19K (CAA→AAA) yibAputative immunity protein for polymorphic toxin RhsA, HEAT‑domain protein, lethality reduction protein
Reads supporting (aligned to +/- strand):  ref base C (19/21);  new base A (4/6);  total (23/27)
Fisher's exact test for biased strand distribution p-value = 7.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.85e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CACACAGAAAGCCTGGAATTGTCGTCACTCCAGACAGTCAAACGATAAAAAAAGATAGCCCTTGTGGAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTGGGCAAGACGCTGTTAGATTGGCAATTGAGTTCTGCTCT  >  NC_000913/3766259‑3766528
                                                                                                                                    |                                                                                                                                         
cacacaGAAAGCCTGGAATTGTCGTCACTCCAGACAGTCAAACGATAAAAAAAGATAGCCCTTGTGGAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTa                                                                                                                                     >  2:38175/1‑139 (MQ=255)
cacacaGAAAGCCTGGAATTGTCGTCACTCCAGACAGTCAAACGATAAAAAAAGATAGCCCTTGTGGAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTa                                                                                                                                     <  2:34595/139‑1 (MQ=255)
   acaGAAAGCCTGGAATTGTCGTCACTCCAGACAGTCAAACGATAAAAAAAGATAGCCCTTGTGGAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGa                                                                                                                                  >  1:346880/1‑139 (MQ=255)
                aaTTGTCGTCACTCCAGACAGTCAAACGATAAAAAAAGATAGCCCTTGTGGAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAatgatga                                                                                                                     <  1:49039/139‑1 (MQ=255)
                 aTTGTCGTCACTCCAGACAGTCAAACGATAAAAAAAGATAGCCCTTGTGGAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAatgatgat                                                                                                                    >  1:260313/1‑139 (MQ=255)
                     tcgtcACTCCAGACAGTCAAACGATAAAAAAAGATAGCCCTTGTGGAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAat                                                                                                                >  2:262460/1‑139 (MQ=255)
                            tCCAGACAGTCAAACGATAAAAAAAGATAGCCCTTGTGGAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCg                                                                                                         <  2:380391/139‑1 (MQ=255)
                                   aGTCAAACGATAAAAAAAGATAGCCCTTGTGGAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACtt                                                                                                  >  2:200056/1‑139 (MQ=255)
                                     tCAAACGATAAAAAAAGATAGCCCTTGTGGAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTtga                                                                                                >  2:84588/1‑139 (MQ=255)
                                     tCAAACGATAAAAAAAGATAGCCCTTGTGGAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTtga                                                                                                >  1:443547/1‑139 (MQ=255)
                                     tCAAACGATAAAAAAAGATAGCCCTTGTGGAGGTTCCTACAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTACGACACTAAATGATGATGAATTATTTCGCTTACTtga                                                                                                >  1:380899/1‑139 (MQ=255)
                                      cAAACGATAAAAAAAGATAGCCCTTGTGGAGGTTCCTGCAATGTTAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTtgat                                                                                               <  1:122591/139‑1 (MQ=255)
                                      cAAACGATAAAAAAAGATAGCCCTTGTGGAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTtgat                                                                                               <  2:41001/139‑1 (MQ=40)
                                      cAAACGATAAAAAAAGATAGCCCTTGTGGAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTtgat                                                                                               <  1:38175/139‑1 (MQ=255)
                                      cAAACGATAAAAAAAGATAGCCCTTGTGGAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTtgat                                                                                               <  1:200056/139‑1 (MQ=255)
                                          cGATAAAAAAAGATAGCCCTTGTGGAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATc                                                                                           <  1:380398/139‑1 (MQ=40)
                                               aaaaaaGATAGCCCTTGTGGAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAAt                                                                                      >  2:74006/1‑139 (MQ=255)
                                               aaaaaaGATAGCCCTTGTGGAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAAt                                                                                      >  2:243596/1‑139 (MQ=40)
                                                                 ggATGTTACTGCAAAGGCAAAGACAAACCAGAAAAGAAAGGCTAGTAAAGAGTATGCGTTATATAATCAATGTCCGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATGTCa                                                                    <  1:481929/139‑1 (MQ=11)
                                                                 ggAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCa                                                                    <  1:243596/139‑1 (MQ=34)
                                                                   aGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATc                                                                  <  2:380899/139‑1 (MQ=34)
                                                                        ccTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCa                                                             <  1:84588/139‑1 (MQ=37)
                                                                          tGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCaga                                                           >  2:252740/1‑139 (MQ=37)
                                                                             aaTGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTa                                                        <  1:252740/139‑1 (MQ=35)
                                                                                gTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTa                                                     <  1:74006/139‑1 (MQ=37)
                                                                                gTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTa                                                     <  2:12297/139‑1 (MQ=37)
                                                                                gTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTa                                                     <  1:262460/139‑1 (MQ=37)
                                                                                           acCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTtgat                                                                                               <  1:273908/86‑1 (MQ=33)
                                                                                           acCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTtgat                                                                                               >  2:273908/1‑86 (MQ=35)
                                                                                           acCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAgg                                          >  2:32747/1‑139 (MQ=34)
                                                                                           acCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGAATTACTGTTAaaagc                                          >  1:285070/1‑138 (MQ=255)
                                                                                             cAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATAAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTg                                        >  2:16527/1‑139 (MQ=14)
                                                                                                aaaagaaaGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTGGGc                                     >  2:178078/1‑139 (MQ=38)
                                                                                                aaaagaaaGGCAAGTAAAGAGTATGGTTTATATAATAAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTGGGc                                     <  2:405269/139‑1 (MQ=17)
                                                                                                    gaaagGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTGGGCAAGa                                 <  1:32747/139‑1 (MQ=38)
                                                                                                    gaaagGCAAGTAAAGAGTATGGTTTATATAATAAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTGGGCAAGa                                 <  1:139666/139‑1 (MQ=17)
                                                                                                              tAAAGAGTATGGTTTATATAATAAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTGGGCAAGACGCTGTTAGa                       >  1:106115/1‑139 (MQ=14)
                                                                                                                  gagTATGGTTTATATAATAAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTGGGCAAGACGCTGTTAGATTgg                   <  2:151384/139‑1 (MQ=17)
                                                                                                                   agTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTGGGCAAGACGCTGTTAGATTGGc                  >  2:135470/1‑139 (MQ=40)
                                                                                                                     tATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTGGGCAAGACGCTGTTAGATTGGCaa                >  1:167839/1‑139 (MQ=37)
                                                                                                                       tGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTGGGCAAGACGCTGTTAGATTGGCAAtt              <  2:346880/139‑1 (MQ=37)
                                                                                                                       tGGTTTATATAATAAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTGGGCAAGACGCTGTTAGATTGGCAAtt              <  2:81337/139‑1 (MQ=14)
                                                                                                                       tGGTTTATATAATAAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTGGGCAAGACGCTGTTAGATTGGCAAtt              <  2:106115/139‑1 (MQ=18)
                                                                                                                            tatataATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTGGGCAAGACGCTGTTAGATTGGCAATTGAGtt         <  1:444099/139‑1 (MQ=40)
                                                                                                                             atataATAAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTGGGCAAGACGCTGtt                          <  1:404152/121‑1 (MQ=18)
                                                                                                                             atataATAAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTGGGCAAGACGCTGtt                          >  2:404152/1‑121 (MQ=17)
                                                                                                                             atataATAAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTGGGCAAGACGCTGTTAGATTGGCAATTGAGTTc        >  2:498466/1‑139 (MQ=21)
                                                                                                                                   tCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTa                                                     <  2:380569/88‑1 (MQ=37)
                                                                                                                                   tCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTa                                                     >  1:380569/1‑88 (MQ=37)
                                                                                                                                   tCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTGGGCAAGACGCTGTTAGATTGGCAATTGAGTTCTGctct  >  1:56629/1‑139 (MQ=255)
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CACACAGAAAGCCTGGAATTGTCGTCACTCCAGACAGTCAAACGATAAAAAAAGATAGCCCTTGTGGAGGTTCCTGCAATGTCAAATACATACCAGAAAAGAAAGGCAAGTAAAGAGTATGGTTTATATAATCAATGTAAGAAACTAAATGATGATGAATTATTTCGCTTACTTGATGATCACAATTCCTTGAAAAGGATTTCATCTGCCAGAGTATTACAGTTAAGAGGTGGGCAAGACGCTGTTAGATTGGCAATTGAGTTCTGCTCT  >  NC_000913/3766259‑3766528

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑