Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,434,8820TG52.3% 47.8 / 71.9 44Y252S (TAC→TCC) truAtRNA pseudouridine(38‑40) synthase
Reads supporting (aligned to +/- strand):  ref base T (7/14);  new base G (23/0);  total (30/14)
Fisher's exact test for biased strand distribution p-value = 1.01e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-08

ATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACC  >  NC_000913/2434742‑2435028
                                                                                                                                            |                                                                                                                                                  
atTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATAATAACGGGCAGGGTGAACCACcgc                                                                                                                                          >  2:699187/1‑151 (MQ=255)
       tATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGAACAAACAGGCCAGGGGGAACAACCGCCAcc                                                                                                                                      >  2:398335/1‑148 (MQ=255)
           ccTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACa                                                                                                                               <  2:713334/151‑1 (MQ=255)
                  cTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAAAACATACCGGGCAGGGGAAACCACCCCGCCCCAATACAAcccct                                                                                                                         >  2:530101/1‑148 (MQ=255)
                      tCATCTTTCAGGCTGTAACCACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGGAGATCATAACCGTCAGGGGAATCCACCCCGACCCGATACAGCCCTTcc                                                                                                                       >  2:86634/1‑148 (MQ=255)
                          cTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCCGGCCGGGGAATCCACCCCGACCAGATACAACCCCTCCGCcttt                                                                                                                 >  2:219928/1‑150 (MQ=255)
                             tCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCGGTCAGGGGAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTTcc                                                                                                              >  1:129527/1‑150 (MQ=255)
                               aGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGAACATACCGGTCAGGGTAATCCACCGCGACCAAAGACAACCCCTcccc                                                                                                                     >  2:289693/1‑139 (MQ=255)
                                    gTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTtgctgc                                                                                                      <  1:259188/151‑1 (MQ=255)
                                          aCGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATAACCGTCAGGGGAATCCACCCCGCCCAGAGAAAGCCCCTCCCCCTTTTCCGTTGCTgccccc                                                                                                  >  2:433863/1‑149 (MQ=255)
                                          aCGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGGAATCCACCGCGACCAGATACAGCCCTTCCCCTTTTGCCGGTTCTgccccc                                                                                                  >  1:257974/1‑149 (MQ=255)
                                             ttGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATAACCGGCAGGGGAATTCACCCCCACCAGAAACAGCCCTTCCCCTTTTTCCGTTTCTGccgcccgc                                                                                               >  2:362229/1‑149 (MQ=255)
                                                  tACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCGGTCAGGGGAATCCACCCCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCcgcggt                                                                                            >  1:278395/1‑145 (MQ=255)
                                                   aCAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCCGGCAGGGGAAACCACCCCGACCAGATACAGCCCTTCCGCTTTTTCCGTTGCTGCCCCCAGCGTTCTGt                                                                                        >  1:689255/1‑150 (MQ=255)
                                                     aGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGGTTTTGGAGATCATAACCGGCAGGGGAATTCACCGCGGCCAGAAACAGCCCTTCCGCTTTTTACGGTGCTGCCGCCAGCGTTCTGTcc                                                                                      >  2:692881/1‑150 (MQ=255)
                                                         tGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATTATACCGGGCAGGGGAATCCACCGCGGCCAGATACAGCCCTTTCGCTTTTGCCCTTGCTGCCGCCACCGTTCTGTCCttt                                                                                   >  2:193288/1‑149 (MQ=255)
                                                               gTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCa                                                                            <  1:359853/150‑1 (MQ=255)
                                                                   cGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCGGTCAGGGGAAACCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCCCCCGCGTTCTGTTCTTTgccgcc                                                                             >  1:310544/1‑145 (MQ=255)
                                                                       cATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATAACGGGCAGGGGAAACCACCGCGGCCAGATAAAGCCCCTCCCCTTTTGCCGTTGGTGCCGCCCGCGCTCTGTCCTTTGCCGCCCGCaa                                                                        >  1:571555/1‑146 (MQ=255)
                                                                         ttattCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGAGCATAACGGGCAGGGGAATACACCCCGACCAGATACAGCCCTTCCGCTTTTGCCCTTGCTGCCGCCCGCGGTCTGTCCTTTgccgcc                                                                             >  2:141206/1‑139 (MQ=255)
                                                                         ttattCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTgccgcc                                                                             <  1:141209/139‑1 (MQ=255)
                                                                          tattCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCGGGCCGGGGAATCCACCGCGACCAGATACAGCCCTTCCCCTTTTTCCGGTGCTGCCGCCAGCGTTCTTTCCTTTGCCGCCCGCCActc                                                                     >  2:391568/1‑146 (MQ=255)
                                                                           attCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTa                                                                <  1:73563/150‑1 (MQ=255)
                                                                               tcGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGACGATCATACAGGTCAGGGGAATCCACCGCGACCCGATACAGCCCTTCCGCTTTTGGCGGTGCTGGCGCCAGCGTTCTTTTCTTTGCCGCCCGCAACTCCGCTAttc                                                             >  2:110715/1‑147 (MQ=255)
                                                                                cGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAg                                                           <  1:641837/150‑1 (MQ=255)
                                                                                  ttAGCCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTCGAAGATCATACCGGCCAGGGGAATCCCCCGCGAACATATACAATCCTTTCGCCTTTGCCCCTGCTGCCCCCAGCGTTCTGTTCTTTTTCCCCGGCACCTCCGCCATCCaaccc                                                        >  2:255028/1‑147 (MQ=255)
                                                                                    aGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCGGTCAGGGGAATCCACCGCGACCAGAAACAGCCCTTCCGCTTTTTCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCtctc                                                      >  1:71040/1‑151 (MQ=255)
                                                                                    aGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGctct                                                       <  1:86635/150‑1 (MQ=255)
                                                                                       ccGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGACGATCCTACCCGTCCGGGGAATCCACCGCGCCCAGATAAAGCCCCTCCGCTTTTTCCCTTGCTGCCGCCCGCGCTCTCTCCCTTTCCGCCCGCCACTCTCCTATTCAGCTcccc                                                     >  2:425608/1‑149 (MQ=255)
                                                                                          ccAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAACATACCGGGCAGGGGAAACCACCGCGCCCAGATACAGCCCTTCCCCCTTTTCCGGTGCTGCCCCCAGCGGTCTGTCCCTTTCCCCCAGCAACTCTGCTATCCCGCTCTCCGGccg                                                >  2:632546/1‑149 (MQ=255)
                                                                                            aGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCGGTCAGGGGAATCCACCGCGACCACAAACAGCCCTTCCCCTTTTTCCGTTGCTGTCGCCCGCGTTCTGTCCTTTGCCGCCCGCAACTCTGCTATCCAACTCTCCCGCTgg                                               >  1:428437/1‑150 (MQ=255)
                                                                                              aaaTAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCGGTCAGGGGAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTTCCGTTGCTGCCCCCAGCGGTCTGTCCTTTGCCGCCAGCAAATCTGCTTTCCCGCTCTCCGGCTGGtt                                             >  1:33329/1‑150 (MQ=255)
                                                                                              aaaTAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCGGTCAGGGTAAACCACCGCGACCAGATACAACCCCTCCCCTTTTGCCGTTGCTGCCCCCCGCGTTCTGTCCTTTTCCGCCCGCCAATCTGCTATCCAGCTCTCCCGCTgggt                                             >  1:446179/1‑148 (MQ=255)
                                                                                                aTAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTtgtg                                          <  2:517970/151‑1 (MQ=255)
                                                                                                                 ggTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATc                          >  2:304384/1‑150 (MQ=255)
                                                                                                                 ggTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATc                          >  1:689300/1‑150 (MQ=255)
                                                                                                                  gTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATc                          >  1:68826/1‑149 (MQ=255)
                                                                                                                   ttttGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAgg                       >  2:2717/1‑151 (MQ=255)
                                                                                                                           gATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGAc               <  1:100596/151‑1 (MQ=255)
                                                                                                                            aTCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACa              <  2:244761/151‑1 (MQ=255)
                                                                                                                                   cGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGGCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTcc       <  1:602235/151‑1 (MQ=255)
                                                                                                                                   cGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTcc       <  1:128710/151‑1 (MQ=255)
                                                                                                                                        aGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGAcc  <  1:581564/151‑1 (MQ=255)
                                                                                                                                        aGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGAcc  <  2:683018/151‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                                  
ATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACC  >  NC_000913/2434742‑2435028

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑