Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,434,882	0	T	G	43.8%	76.0 / 19.0	50	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
Reads supporting (aligned to +/- strand):  ref base T (4/23);  new base G (21/0);  total (27/23)
Fisher's exact test for biased strand distribution p-value = 5.78e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACC  >  NC_000913/2434733‑2435028                                                                                                                                                       |                                                                                                                                                   cAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTa                                                                                                                                                   <  1:221442/151‑1 (MQ=255)      ccATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATcc                                                                                                                                               <  1:651713/150‑1 (MQ=255)          atTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCAAACCGGGCAGGGGAAATCAcc                                                                                                                                            >  1:887549/1‑149 (MQ=255)            ttGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACcgcg                                                                                                                                         <  2:24736/150‑1 (MQ=255)             tGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATAACGGTCAGGGGAAaccacc                                                                                                                                            >  1:442579/1‑146 (MQ=255)                  aTGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGTAGATTATAACGGTCAGGGGAATCCACCGCGAcc                                                                                                                                      >  2:182706/1‑147 (MQ=255)                   tGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCCTACCGGTCAGGGGAATCCACCGCGACCa                                                                                                                                     >  1:508767/1‑147 (MQ=255)                   tGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATAACGGGCAGGGGAATCCACCGCGACCa                                                                                                                                     >  1:144973/1‑147 (MQ=255)                    gCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATAc                                                                                                                                <  1:153892/151‑1 (MQ=255)                        tGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGGAGATCATACCGGTCAGGGGAATCCACCCCGACCAGATACAGcc                                                                                                                            >  1:267085/1‑151 (MQ=255)                            cTCGTCATCTTTCAGGCTGT‑ACTAACGTGGCCACCGCCTTGAATGCTTCCAGCATTCTTCTCGGTTAGCCCGCCAGAATAACCGGCCCAATTGGCGGTTTTGGAAAAAAAACCCGGTCAGGGGAATCCACCCGCACCCGAAACACCCCtt                                                                                                                         >  2:231745/1‑150 (MQ=255)                               gTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACAAGCCAGGGGAAACCCCCCCGCCCACATAAAAccccttc                                                                                                                       >  2:565609/1‑145 (MQ=255)                               gTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGGAATCCACCGCGACCCGATACAGCCCTTcc                                                                                                                       >  1:125873/1‑149 (MQ=255)                               gTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGGTTTTGAAGATCATAACGGGCAGGGGAATCCCCCGCGACCAGATACAACCCTTcc                                                                                                                       >  2:251010/1‑149 (MQ=255)                                      ttCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTg                                                                                                                <  1:745223/149‑1 (MQ=255)                                      ttCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGc                                                                                                               <  2:721531/150‑1 (MQ=255)                                      ttCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGATTTTGGAGATCATACCCGGCAGGGGGAATCACCGCGACCAGATACAGGCCTTCCGCtttttt                                                                                                               >  2:600647/1‑148 (MQ=255)                                         aGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGtt                                                                                                           <  2:270996/151‑1 (MQ=255)                                              gTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGCTTTTGAAGATCATAACCGTTAGCGCAATCCACCCCGCCCACAGACAGCCCCCCCCCTTTTGcc                                                                                                              >  2:735591/1‑143 (MQ=255)                                                    aCGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGGAATCCACCGCGACCAGATACAACCCTTCCGCTTTTTCCGTTGCTgccgcc                                                                                                  >  1:388421/1‑149 (MQ=255)                                                           cTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAAATCATAACCGTAAGGGGAAAACACCACGACCAGATAAAGCCCCTCCGCTTTTTCCGGTTCTGCCGCCCACGTTc                                                                                           >  1:572067/1‑149 (MQ=255)                                                                 ccTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCttt                                                                                   <  1:685441/151‑1 (MQ=255)                                                                               aGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGGAGATCATAACCGTTAGGGCAATCCACCGCGACCAGATACACCCCCTCCCCTTTTTTCGTTGGTGTCGGCCGCGGTCTTTCCTTTTCCGCCCGCAAatc                                                                     >  1:951556/1‑151 (MQ=255)                                                                               aGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAActc                                                                     <  2:869415/151‑1 (MQ=255)                                                                                gCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAActct                                                                    <  2:78013/151‑1 (MQ=255)                                                                                 cATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATAACGGGCCGGGGAATCCACCCCGACCAGATAAAGCCCTTCCGCCTTTGCCGCTGCTGCCGCCCGCGTTTTGTCCCTTTCCGCCAGCaa                                                                        >  1:513802/1‑146 (MQ=255)                                                                                    tattCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGAACCTACCGGTCAGGGGAATCCACCGCGACCAGATACAGCCCTTCCGCCTTTGCCGTTGCTGCCCCCAGCGGTCTGTCCTTTGCCCCCAGCAACTCCGCt                                                                 >  2:653091/1‑150 (MQ=255)                                                                                      ttCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTAt                                                               <  2:254418/150‑1 (MQ=255)                                                                                               aGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCtctc                                                      <  2:47592/151‑1 (MQ=255)                                                                                                 tCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCCGTCAGGGGAATCCACCCCGGCCAGATACAACCCTTCCGCTTTTTCCGTTGCTGCCGCCCGCGTTCTGTCCTTTGCCGCCCGCAACTCTGCTATcacatcgg                                                       >  1:735981/1‑141 (MQ=255)                                                                                                 tCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATc                                                              <  2:735799/141‑1 (MQ=255)                                                                                                  ccGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGGAGATTATAACCGGCAGGGGAAAACACCGCGACCAGATACAGCCCTTCCCCTTTTTCCGTTGCTGCCGCCCGCGTTCTGTCCTTTTCCGCCCGCAACTCTGCTATCCAGCCCTcc                                                     >  2:417046/1‑149 (MQ=255)                                                                                                   cGCCAGAAATAGCGGGCCCATTGGCGGGTTTTGGAGATCACACCCGGCACGGTAAAACAACCCCACCAGATACAACCCTTCCGCTTTTTCCGGTTCTGGCCCCCGCCGTCTTTCCTTTTCCGCCCGCAACTCCTCTATCCCGCCCTcc                                                     >  2:19329/1‑148 (MQ=255)                                                                                                    gCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATAACGGGCAGGGGAATCCACCGCGACCAGATACAGCCCCTCCGCTTTTTCCGTTGCTGCCGCCAGCGGTCTGTCCTTTTCCGCCAGCAACTCTGCTATCCAGCTCTCCgg                                                   >  1:400866/1‑149 (MQ=255)                                                                                                     ccAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTg                                                <  2:333823/151‑1 (MQ=255)                                                                                                      cAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTgg                                               <  1:653257/151‑1 (MQ=255)                                                                                                        gAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATAACGGTCAGGGGAATTCACCGCGACCCGAAACAGCCCCTCCCCTTTTGCCGTTTGTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACACTGTTTTCCAACTCTTCGGCTGGtt                                             >  1:667110/1‑151 (MQ=255)                                                                                                             aGCGGGCCCATTGGCGGTTTTGGGAGATCCTACCGGGTAGGGGAATACACCCCGACCCGATACAGCCCCTCCGCCTTTTCCCTTGCTGCCCCCAGCGGTATGTCCTTTGTCGCCCCCAACCCCTCTATCCCGCTCTCCGGCTGGTTGTggg                                        >  2:300448/1‑151 (MQ=255)                                                                                                              gCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGc                                       <  1:224928/151‑1 (MQ=255)                                                                                                               cGGGCCCATTGGCGGTTTTGGAAGATCATTCCGGGTCGGGGAATCCCCCGCGGCCAGATACAGCCCTTCCGCCTTTTCCGGTGCTGCCCCCAGCGTTTTGCCCCTTTCCGCCCGCAACTCTGCTTTCCACCCCTCCGGCTGGGTGTggg                                        >  2:804516/1‑149 (MQ=255)                                                                                                                    ccATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGAc                                 <  1:908884/151‑1 (MQ=255)                                                                                                                        tGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTcc                             >  2:656371/1‑151 (MQ=255)                                                                                                                          gCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCAt                           <  1:894067/151‑1 (MQ=255)                                                                                                                          gCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCCTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCAt                           >  2:195841/1‑151 (MQ=255)                                                                                                                               tttGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGc                      >  2:450903/1‑151 (MQ=255)                                                                                                                                 tGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCt                     <  1:365931/150‑1 (MQ=255)                                                                                                                                   gAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGcc                  <  2:701403/151‑1 (MQ=255)                                                                                                                                          aTACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAata           <  2:398609/151‑1 (MQ=255)                                                                                                                                                gTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTg     <  1:977063/151‑1 (MQ=255)                                                                                                                                                   aGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGAcc  <  1:940405/151‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                   CAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTC‑GTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACC  >  NC_000913/2434733‑2435028

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: ‑