Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,434,882	0	T	G	49.0%	53.0 / 22.2	51	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
Reads supporting (aligned to +/- strand):  ref base T (8/18);  new base G (25/0);  total (33/18)
Fisher's exact test for biased strand distribution p-value = 7.32e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCAT  >  NC_000913/2434738‑2435030                                                                                                                                                   |                                                                                                                                                      ccATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGATCATA‑CCGGTCAGGGTAATcc                                                                                                                                                  <  2:208963/150‑1 (MQ=255) ccATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGAACATA‑ACGGGCAGGGGaa                                                                                                                                                     >  1:219534/1‑147 (MQ=255)         gCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTTGTAGATAATA‑ACGGTGAGGGGAATCCACccc‑gggc                                                                                                                                        >  2:126637/1‑148 (MQ=255)              tGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGGAGAACATA‑CCTGGCAGGGTAAGCCACcgctcccacat                                                                                                                                     >  1:212697/1‑142 (MQ=255)                 cTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑GTTTGGAAGATTATC‑ACGGGCAGGGGAATACACCGC‑GACCAGaaaac                                                                                                                                 >  2:57829/1‑146 (MQ=255)                     tACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTTGGAGAATATA‑ACGGTCAAGGGAAAACACCCCGGACCAgttcaa                                                                                                                                 >  2:109699/1‑142 (MQ=255)                     tACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGATCATA‑CCCGGCAGGGGAATACACCCC‑GACCAGATACAGccc                                                                                                                             >  2:584161/1‑150 (MQ=255)                          gTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑GTTTTGAAGACCATA‑ACCGGCAGGGGAAACAACCCC‑GCCCAGATAAAGCCCCTCCGc                                                                                                                       >  2:565046/1‑151 (MQ=255)                           tCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTc                                                                                                                          <  1:259213/147‑1 (MQ=255)                            cATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTTGAAGATCATA‑CCCGTCAGGGGAATCCACCCC‑GACCAGAAACAGCCCCTCCCCtt                                                                                                                     >  1:387352/1‑151 (MQ=255)                                tttCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTTGAAGATCATA‑CCCGGCAGGGGAAACCACCCC‑GACCCGAAAAAGCCCCTCCGCcttt                                                                                                                   >  2:651106/1‑149 (MQ=255)                                 ttCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGc                                                                                                                 <  2:300854/150‑1 (MQ=255)                                      gCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTTGAAGATCATA‑CCGGTCAGGGGAATCCACCCC‑GACCAGAAACAACCCTTCCCCTTTTTCCGt                                                                                                              >  1:666906/1‑148 (MQ=255)                                       cTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTTGGAGAACATA‑CCCGTCAGGGGAATCCACCCC‑GACCCGATACCGACCTTCCGCTTTTTTCGtt                                                                                                             >  2:96296/1‑148 (MQ=255)                                           aaCTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTgccg                                                                                                      <  2:12996/151‑1 (MQ=255)                                             cTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGGAGATCATA‑CCCGGCAGGGGAAACCACCGC‑GACCAGATACAGCCCTTCCCCTTTTTCCGGTGCTgccgcc                                                                                                    >  1:97874/1‑151 (MQ=255)                                              tACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTTGGAGATCATA‑CCCGGCAGGGGAATCCACCCC‑GACCAGATACAACCCCTCCCCCTTTTCCGTTTCTgccccc                                                                                                    >  2:415049/1‑150 (MQ=255)                                                   tGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTTGAAGATCATA‑ACCGTCAGGGTAATCCACCCC‑GACCAGAAACAACCCCTCCCCCTTTGCCCTTGCTGCCGCCCGCGtt                                                                                              >  2:633976/1‑151 (MQ=255)                                                       tACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTTGTAGATCATA‑CCCGTCAGGGGAATACACCCC‑GCCCAGATAAAGCCCTTCCGCTTTTGCCGGTTCTGTCGCCACCGtt                                                                                              >  2:320580/1‑147 (MQ=255)                                                         cAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTTGAAGATCATA‑CCGGGCAGGGGAAACCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCCGTGCTTCCCCCCGCGTTCTGTcc                                                                                        >  2:382579/1‑151 (MQ=255)                                                           gCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCt                                                                                       <  1:158614/150‑1 (MQ=255)                                                               gAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTTTAAGTTCATA‑CCCGTGAGGGTAAAACCCCGC‑GACCCGATACAGCCCTTCCCCCTTTTCCGGTTCTGCCCCCCCCGTTCttttcctt                                                                                     >  2:222677/1‑141 (MQ=255)                                                                aaaTGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTgccg                                                                                 <  1:695124/151‑1 (MQ=255)                                                                aaaTGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTgccg                                                                                 <  1:37759/151‑1 (MQ=255)                                                                  aTGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTgccgcc                                                                               <  2:245505/151‑1 (MQ=255)                                                                   tGTTCCGAGCATTATTCTCGTTAGTCCGCTAGAAATAGCGGGCCCATTGGCGG‑TTTTTTTAGATTATA‑ACGGTCAGTGGAATCCCCCTC‑GACCGCAAACCACCCCTCCGCCTTTGTCGTTGCTCCACCCCGCGTTCTGTCCttttgtccc                                                                               >  2:710326/1‑144 (MQ=255)                                                                        cGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGATCATA‑CCGGGCAGGGGAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCaa                                                                          >  1:580885/1‑150 (MQ=255)                                                                            cATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTTGTAGATCATA‑CCCGTCCGGGTAATCCACCCC‑GCCCCGATACAACCCCTCCGCTTTTGCCGTTGCTTCCCCCCCCGTTCTTTCCTTTTCCGCCAGCCAc                                                                         >  2:534916/1‑147 (MQ=255)                                                                             attattCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTTGGAGGTCATA‑CCGGTCCGGGGAAACCACCCC‑GGCCAGATACAACCCTTCCGCTTTTTCCGTTTCTGCCGCCCGCGGTCTGTCCTTTTCCCCCAGCAActc                                                                       >  2:528573/1‑148 (MQ=255)                                                                               tattCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTTGTAGATCATACCCGGCAAGGGGAAACACCCCC‑GCCCAAAACCAACCC‑TCCGCTTTTTTCCTTGCTGGCGCCCCCGGTCTGTCCtttttccccc                                                                              >  2:50886/1‑132 (MQ=255)                                                                                     cGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGC‑GTCCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCa                                                              <  2:70942/149‑1 (MQ=255)                                                                                     cGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAg                                                             <  1:419922/150‑1 (MQ=255)                                                                                      gTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTTGGAGATCATA‑CCGGGCAGGGGAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTTCCGGTGGTGCCCCCCGCGTTCTGTCCTTTTCCGCCCGCAAATCTTCTATcc                                                               >  1:122086/1‑147 (MQ=255)                                                                                      gTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGct                                                           <  1:679589/151‑1 (MQ=255)                                                                                       ttAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGATAATA‑CCGGTCAGGGGAAACCACCGC‑GACCAGATACAGCCCTTCCCCTTTTTCCGGTGCTGCCGCCAGCGGTCTGTCCTTTTCCGCCCGCAACCCTGCTTTCCAGc                                                            >  2:3216/1‑149 (MQ=255)                                                                                            ccGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCgg                                                     <  2:701979/151‑1 (MQ=255)                                                                                            ccGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCgg                                                     <  2:65123/151‑1 (MQ=255)                                                                                               ccAGAAATAGCGGGCCCATTGGCGG‑TTTTTGAAAATCAAA‑CCCGTCAGGGGAATCCACCGC‑GACCAGATACAGCCCTTCCCCCTTTTCCGTTGCTGCCCCCAGCGGTCTGTCCTTTGCCGCCAGCAACTCTGCCATCCAGCTCTcccg                                                     >  2:650351/1‑146 (MQ=255)                                                                                                 aGAAATAGCGGGCCCATTGGCGGCTTTTGGAGGA‑AATT‑CCCGTCCGGGGAATCCACCCC‑CACACGCTACAACCCTTCCGCCTTTTCCGCTTCGGCCACCCGCGCCTTTTCCTTTTGCGCCAGCAACCCCGGTATCCacgcctcccg                                                     >  1:523155/1‑137 (MQ=255)                                                                                                   aaaTAGCGGGCCCATTGGCGG‑TTTTGGAAGAACATA‑CCGGTCAGGGGAATCCACCCC‑GCCCCGATACAGCCCCTCCCCTTTTTCCGGTGCTGCCGCCCGCGGTCTGTCCTTTTCCGCCCGCAAATCTGCTATCCCGCTCTCCGGCTgg                                                 >  2:600297/1‑148 (MQ=255)                                                                                                    aaTAGCGGGCCCATTGGCGG‑TTTTTGGAGAGCATA‑CCCGGCAAGGTAATTCACCGC‑GAACCGAAACAGGCCCTCCGCTTTTTCCCTTTCTGCCCCCCGCGGTTTGTTCTTTTCCGCCCCCCACTCTGCTCTCCCGcccccc                                                       >  2:84806/1‑136 (MQ=255)                                                                                                     aTAGCGGGCCCATTGGCGG‑TTTTGGAAGATCATA‑CCGGTCAGGGGAATCCACCGC‑GACCAGATACAGCCCTTCCCCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCCGCAACTCTGCTATCCAGCTCTCCGGCTgggt                                               >  1:245189/1‑146 (MQ=255)                                                                                                            gCCCATTGGCGG‑TTTTGGAAGATCATA‑CCGGTCAGGGGAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTTCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCAcc                                      >  1:289382/1‑150 (MQ=255)                                                                                                                       g‑TTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAg                          <  2:522658/151‑1 (MQ=255)                                                                                                                               aaGATCATA‑CCGGTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCg                   <  1:589430/151‑1 (MQ=255)                                                                                                                                   tCATA‑CCGGTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACa                >  2:382711/1‑150 (MQ=255)                                                                                                                                       a‑CCGGTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAatat            <  2:202378/150‑1 (MQ=255)                                                                                                                                          cGGTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTcc         >  1:176705/1‑151 (MQ=255)                                                                                                                                            gTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTg       <  1:512418/151‑1 (MQ=255)                                                                                                                                               aGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGAcc    >  1:52633/1‑151 (MQ=255)                                                                                                                                                 ggTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTTCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCag  <  2:589503/151‑2 (MQ=255)                                                                                                                                                   |                                                                                                                                                      CCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGG‑TTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGC‑GACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCAT  >  NC_000913/2434738‑2435030

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑