Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,434,8820TG44.0% 14.2 / 10.9 25Y252S (TAC→TCC) truAtRNA pseudouridine(38‑40) synthase
Reads supporting (aligned to +/- strand):  ref base T (5/9);  new base G (11/0);  total (16/9)
Fisher's exact test for biased strand distribution p-value = 1.01e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TGGCATAAACCCAGACGCCGTACTCCGCGACCAGCTCTGCCAGATGCACGTCAATGTGCAGGATAAAATCGATGAGGAAATAAATCAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACC‑AGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACAAAAGCATTCGCTTTAATATCTACCACCACATAAGGACCGTGACGCGTGACATTAATATGCATAACGTTGCGCCACGGGGTTCGGGACTGGC  >  NC_000913/2434648‑2435131
                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                          
tGGCATAAACCCAGACGCCGTACTCCGCGACCAGCTCTGCCAGATGCACGTCAATGTGCAGGATAAAATCGATGAGGAAATAAATCAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGAACATACCGGTCAGGGGAATCCACCGCGAcc                                                                                                                                                                                                                                              >  1:12734/1‑249 (MQ=255)
      aaaCCCAGACGCCGTACTCCGCGACCAGCTCTGCCAGATGCACGTCAATGTGCAGGATAAAATCGATGAGGAAATAAATCAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCGGTCAGGGGAAACCACCCCGACC‑AGAAACa                                                                                                                                                                                                                                      >  2:54164/1‑250 (MQ=255)
        aCCCAGACGCCGTACTCCGCGACCAGCTCTGCCAGATGCACGTCAATGTGCAGGATAAAATCGATGAGGAAATAAATCAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGTAGATCATACCCGTCCGGGGAAttcccctccacccgcataaaac                                                                                                                                                                                                                                    >  2:96351/1‑230 (MQ=255)
                           cgACCAGCTCTGCCAGATGCACGTCAATGTGCAGGATAAAATCGATGAGGAAATAAATCAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACC‑AGATACAGCCCTTCCGCTTTTGCCGTtgc                                                                                                                                                                                                                <  1:372361/251‑1 (MQ=255)
                                aGCTCTGCCAGATGCACGTCAATGTGCAGGATAAAATCGATGAGGAAATAAATCAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATTATACCGGTCAGGGTAATCCACCCCGCCCCACA‑AAAGCCCCTCCGCTTTTGCCGGtgctggcc                                                                                                                                                                                                           >  2:195917/1‑248 (MQ=255)
                                        cAGATGCACGTCAATGTGCAGGATAAAATCGATGAGGAAATAAATCAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGAATATAACGGGCAGGGGAATCCACCCCGGCC‑CGATACCGCCCTTCCGCTTTTTCCGTTGCCTCCGCCAGCggt                                                                                                                                                                                                   >  2:343172/1‑249 (MQ=255)
                                                                 aaaTCGATGAGGAAATAAATCAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGGTCATACCGGTCAGGGGAATCCACCGCGACC‑CGATAAAACCCTTCCCCTTTTTCCGGTGGTGCCGCCCGCGGTCTGTCCTTTTCCGCCAGCAActcct                                                                                                                                                                          >  2:108452/1‑249 (MQ=255)
                                                                         gAGGAAATAAATCAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATAACGGGCAGGGGAATCCACCCCGACC‑AGATACAACCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTTCCTTGCCGCCACCAACTCCTCTATcccg                                                                                                                                                                  >  1:289547/1‑249 (MQ=255)
                                                                                           cATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAACATACCGGGCAGGGGAATCCAACGCGCCC‑AGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCCGCGTTCTGGCCTTTTCCGCCCGCAACTCTGCTATCCCGCTCTCCCGCTGGTTGTgg                                                                                                                                                >  1:288253/1‑251 (MQ=255)
                                                                                              atTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACC‑AGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCa                                                                                                                                             <  1:293255/251‑1 (MQ=255)
                                                                                                             gTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACC‑AGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAg                                                                                                                               <  2:19466/250‑1 (MQ=255)
                                                                                                                   gTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGCGCAGTATTCTCGTTCGTCCGCCAGAAATAACGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACC‑AGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCg                                                                                                                        <  2:32049/251‑1 (MQ=255)
                                                                                                                   gTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGGAGATCATACCGGGCAGGGGAATCCACCGCGACC‑AGATACAGCCCTTCCGCTTTTTCCGTTTCTGCCGCCCGCGTTCTGTCCttttc                                                                                                                                                                                        >  1:129700/1‑185 (MQ=255)
                                                                                                                   gTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACC‑AGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTgc                                                                                                                                                                                        <  2:129700/187‑1 (MQ=255)
                                                                                                                     cATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACC‑AGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGAc                                                                                                                      <  2:127748/251‑1 (MQ=255)
                                                                                                                                                         aactGTTCCGCGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGCAGATTATTCCGGTCAGGGTAATACCCCCCGACC‑AGATACCGCCCTTCCGCCTTTTTCGGTGCTGCCCCCAGCGGTCTGTCCCTTTCCGCCCGCACATCTGCTATCCCGCCCTCCGGCTGGTTGGGGGGCCCCACCTCCATTAGGCCTCCCCCAATATTCCTCACCATATGCTGTTCCAAAACATTccc                                                                                  >  2:48600/4‑249 (MQ=255)
                                                                                                                                                         aaaTGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATTATACCGGTGAGGGTAATCCACCCCGACC‑CGATACAGCCCTTCCCCTTTTTCCCTTGCTTCCCCCAGCGTTTTGTCCTTTTCCGCCAGCCAATCCGCTCTCCCGCCCTCCCGCTGGTTGTGGGCACCCACTTTCATCAGGCCGCCGACCATATTCCTGACCCTATGATGTAACAAAGCATTCGc                                                                                  >  1:69425/1‑251 (MQ=255)
                                                                                                                                                            tGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAAATCATAACGGTCAAGGGAATCCCCCCCCACC‑CGATAAAGCCCTTCCGCTTTTTCCGTTGCTTCCCCCAGCGTTCTTTCCTTTTCCGCCCCCCACTCTTCTTTCCCCCATTCCCGCTTGTTTTGGGCCCCCACTTCCCTCCCGCTGCCCACAATATTTCTGACCATATTATTTACCAAAACAttatcttt                                                                               >  1:358489/1‑245 (MQ=255)
                                                                                                                                                              ttCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGGAATCCACCGCGACC‑AGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCCGCGGTCTGTCCCTTGCCGCCAGCCACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTTCCTCAGGCTGCCGACCATATTCCTTACCCTATGATGTACAAAAACATTCGCTTTa                                                                              >  1:179918/1‑250 (MQ=255)
                                                                                                                                                                                  aGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACC‑AGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACAAAAGCATTCGCTTTAATATCTACCACCACATAAGGa                                                         <  1:317675/251‑1 (MQ=255)
                                                                                                                                                                                   gTCCGCCAGAAATATCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACC‑AGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATAGGATGTACAAAAGCATTCGCTTTAATATCTACCACCACATAAGGa                                                         <  2:294990/250‑1 (MQ=255)
                                                                                                                                                                                    tCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCGGTCAGGGGAATCCACCCCGACC‑CGATACAACCCCTCCGCTTTTTCCGTTGCTGCCGCCCGCGTTCTGTCCTTTGCCGCCAGCCAATCTGCTATTCAGCTCTCCCGCTGGTTGTGGGCCCCCACTTCCATCAGGCTGCCGACCATATTCCTGGCCATATGATGTACAAAAGCATTCGCTTTAATATCTACCACCACCTAAAGAcc                                                       >  1:210321/1‑251 (MQ=255)
                                                                                                                                                                                                               ggTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACC‑AGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACAAAAGCTTTCGCTTTAATATCTACCACCACATAAGGACCGTGACGCGTGACATTAATATGCATAAc                            >  1:86989/1‑251 (MQ=255)
                                                                                                                                                                                                                                 cGGTCAGGGTAATCCACCGCGACC‑AGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACAAAAGCATTCGCTTTAATATCTACCACCACATAAGGACCGTGACGCGTGACATTAATATGCATAACGTTGCGCCACGGGGTTCg          <  1:374829/251‑1 (MQ=255)
                                                                                                                                                                                                                                         gTAATCCACCGCGACC‑AGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACAAAAGCATTCGCTTTAATATCTACCACCACATAAGGACCGTGACGCGTGACATTAATATGCATAACGTTGCGCCACTGGGTTCGGGACTGGc  >  2:200749/1‑251 (MQ=255)
                                                                                                                                                                                                                                          tAATCCACCGCGACC‑AGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACAAAAGCATTCGCTTTAATATCTaccacc                                                                  <  2:265446/186‑1 (MQ=255)
                                                                                                                                                                                                                                          tAATCCACCGCGACC‑AGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACAAAAGCATTCGCTTTAATATCTaccacc                                                                  >  1:265446/1‑186 (MQ=255)
                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                          
TGGCATAAACCCAGACGCCGTACTCCGCGACCAGCTCTGCCAGATGCACGTCAATGTGCAGGATAAAATCGATGAGGAAATAAATCAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACC‑AGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATATGATGTACAAAAGCATTCGCTTTAATATCTACCACCACATAAGGACCGTGACGCGTGACATTAATATGCATAACGTTGCGCCACGGGGTTCGGGACTGGC  >  NC_000913/2434648‑2435131

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑