Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,434,882	0	T	G	45.3%	80.6 / 10.7	53	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
Reads supporting (aligned to +/- strand):  ref base T (6/23);  new base G (24/0);  total (30/23)
Fisher's exact test for biased strand distribution p-value = 7.75e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCA  >  NC_000913/2434733‑2435029                                                                                                                                                       |                                                                                                                                                    cAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGTCAGGGTa                                                                                                                                                    <  2:691167/151‑1 (MQ=255)     tCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGGAGAT‑CATAACGGTCAGGGGAATcc                                                                                                                                                >  2:420153/1‑151 (MQ=255)      ccATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGGTTTTGAAGAT‑CATACCGGGCAGGGGAAttc                                                                                                                                                >  1:915130/1‑148 (MQ=255)        atatTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGAT‑CATAACGGTCAGGGGAATCCAcc                                                                                                                                             >  2:861614/1‑151 (MQ=255)                  aTGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAg                                                                                                                                     <  1:816891/149‑1 (MQ=255)                    gCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGGAGGTGCAT‑CCAGCCCGGGGAAACCACACCGACCAGATa                                                                                                                                  >  1:655523/1‑150 (MQ=255)                    gCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGGT‑CATAAAGGCCCGGGGAATTCAcaccacccacaa                                                                                                                                   >  2:617065/1‑138 (MQ=255)                     ccTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGAT‑AATACCGGTCAGGGGAATACACCCCGACCAGATa                                                                                                                                  >  2:635824/1‑149 (MQ=255)                          tACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGGA‑CATAACGGTCAGGGTAAACCACCGCGCACAGATaaaacc                                                                                                                             >  1:378765/1‑144 (MQ=255)                           aCTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGAT‑CATAACGGGCCGGGGAATCCACCGCGACCCGATACAACCCtt                                                                                                                          >  2:82355/1‑151 (MQ=255)                           aCTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCt                                                                                                                           <  1:680923/150‑1 (MQ=255)                              cGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTc                                                                                                                         <  1:548472/149‑1 (MQ=255)                                tCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGc                                                                                                                      >  2:501648/1‑150 (MQ=255)                                  aTCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGTGAAAT‑CATACCGGTCAGGGGAAAACCCCCCGACCCCATACAACCCCTCCGCctt                                                                                                                   >  1:654476/1‑151 (MQ=255)                                    cTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGAT‑AATACCGGTCAGGGGAATACACCCCGACCAGATACAGCCCCTCCGCttttt                                                                                                                 >  1:414579/1‑150 (MQ=255)                                        cAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGAT‑CATAACCGGCAGGGGAATCCACCCCGACCAGATACAGCCCTTCCGCTTTTGcc                                                                                                               >  1:138541/1‑149 (MQ=255)                                              gTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTtgctg                                                                                                        <  2:732383/150‑1 (MQ=255)                                               tAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGTCAGGGGAATACACCGCGACCAGATACAGCCCCTCCGCTTTTGCCGTTGCTgcc                                                                                                      >  1:151862/1‑151 (MQ=255)                                                  cTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGAA‑GATAACGGTCAGGGGAAACCACCGCGGCCAGATACAGGCCTTCCGCTTTTTCCGTTGCTgccccc                                                                                                   >  2:1026961/1‑151 (MQ=255)                                                   tACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGAT‑TATACCCGTCAGGGGAATCCACCGCGACCAGATAAAGCCCCTCCGCTTTTGCCGTTGCTgccgccc                                                                                                  >  1:125077/1‑150 (MQ=255)                                                    aCGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCa                                                                                                  <  2:766779/150‑1 (MQ=255)                                                     cGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGGAGAT‑CATACCGGTTAGGGGAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCCCCAg                                                                                                 >  2:341196/1‑150 (MQ=255)                                                       ttGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGAT‑CATACCGGTCAGGGTAAACCACCGCGACCAGATACCGCCCCTCCGCTTTTTTCGGTGCTGCCGCCcgcg                                                                                               >  1:32237/1‑150 (MQ=255)                                                          gCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCt                                                                                           <  1:660165/151‑1 (MQ=255)                                                                 ccTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCttt                                                                                    <  2:545203/151‑1 (MQ=255)                                                                   tGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTTAAGAT‑CATAACGGTCAGGGGAAACCACCCCCACCCGGTACAGCCCTTCCGCTTTTGTCGTTGCTGCCGCCCGCGGTCTGCCCtct                                                                                    >  1:653484/1‑147 (MQ=255)                                                                     aaaTGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGAT‑CATACCGGGCAGGGGAATCCAACGCGGCCAGATACAACCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTgcc                                                                                 >  2:538478/1‑150 (MQ=255)                                                                     aaaTGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTgccg                                                                                <  2:543795/151‑1 (MQ=255)                                                                        tGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGAT‑CATACCCGTCAGGGTAATCCACCCCGACCCGATACAGCCCCTCCGCCTTTGTCGCTGCCGCCGCCCGCCCTCTGTCCCTTcccgcc                                                                              >  1:422143/1‑150 (MQ=255)                                                                         gTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCa                                                                             <  2:891395/150‑1 (MQ=255)                                                                             cGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGAA‑CAAAACCGTCAGGGGAAACCACCGCGGCCAGATACAACCCTTCCGCTTTTGCCGGTTCTGCCGCCCGCGTTTTGTCCTTTGCCGCCAGCaa                                                                         >  2:879324/1‑150 (MQ=255)                                                                             cGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGAT‑CATACCGGGCAGGGGAATCCACCGCGACCAGATACAACCCTTCCCCTTTTTCCGTTGCTGCCCCCCGCGTTCTGTCCTTTTCCCCCAGcca                                                                         >  2:816323/1‑148 (MQ=255)                                                                                 cATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGAT‑CATACCGGTCAGGGGAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTTCCGTTGCTGCCGCCAGCGTTCTGTCCTTTTCCGCCCGCAActc                                                                      >  2:680436/1‑149 (MQ=255)                                                                                 cATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGAT‑CATACCGGGCAGGGGAATCCACCGCGACCAGATAAAGCCCTTCCCCTTTTTCCGTTGCTGCCGCCCGCGTTCTGTCCTTTTCCCCCAGCAActc                                                                      >  2:33768/1‑149 (MQ=255)                                                                                  attattCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGAT‑CATACCGGTCAGGGGAATCCACCGCGACCAGATAAAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTTTCCTTTTCCGCCAGCAActc                                                                      >  2:812679/1‑148 (MQ=255)                                                                                        ctcGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGTAGAT‑CATACCGGGCCGGGGAATCCACCGCGACCAGAAACAGCCCCTCCGCTTTTTCCGTTGCTTCCCCCCGCGGTCTTTCCCTTGCCCCCCGCCACCCTCCCATcc                                                              >  1:491518/1‑150 (MQ=255)                                                                                          cGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAg                                                            <  2:512923/150‑1 (MQ=255)                                                                                           gTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGct                                                          <  1:51380/151‑1 (MQ=255)                                                                                               gTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGGCAGGGTAATCCACCGCGACCAGATAAAGCCCTTCCCCTTTTTCCGTTGCTGCCCCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATTCAGCTCTcc                                                      >  2:598871/1‑151 (MQ=255)                                                                                                 ccGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCgg                                                    <  1:40742/151‑1 (MQ=255)                                                                                                 ccGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGGCAGGGGAAACCACCACGACCCAAAACAGCCCTTCCGCTTTTGCCCTTGCTGCCCCCCGCGTTCTGTTCTTTTCCCCCCGCAAACCTGCCATCCAGctc                                                         >  2:275079/1‑146 (MQ=255)                                                                                                     cAGAAATAGCGGGCCCATTGGCGGTTTTGGGAGAT‑CATAACGGGCAGGGGAATCCCCCGCGGACAGGTTCAGCCCCTTCGCTTTTTCCGTTGGTGCCCCCCGGGTTTCGTCCTTTGCCGCCCGCAACTCTTCTTTCCCGCCCTCCGGGTgg                                                >  1:198830/1‑151 (MQ=255)                                                                                                            aGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTggg                                         <  1:968089/151‑1 (MQ=255)                                                                                                                         gCGGTTTTGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCAt                            <  1:975289/151‑1 (MQ=255)                                                                                                                             ttttGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAgg                        >  2:324150/1‑151 (MQ=255)                                                                                                                                tGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCt                      <  2:889326/150‑1 (MQ=255)                                                                                                                                   aaGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCg                  <  1:934891/151‑1 (MQ=255)                                                                                                                                          aTACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACaa              <  1:132579/149‑1 (MQ=255)                                                                                                                                            aCCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATAtt          <  1:519119/151‑1 (MQ=255)                                                                                                                                             ccGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTc         <  2:543743/151‑1 (MQ=255)                                                                                                                                             ccGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTc         <  1:543314/151‑1 (MQ=255)                                                                                                                                                gTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTg      <  2:121996/151‑1 (MQ=255)                                                                                                                                                    gggTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCa  <  2:26323/151‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                    CAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGAT‑CATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCA  >  NC_000913/2434733‑2435029

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑