Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,434,861	0	G	T	46.9%	46.6 / 32.1	49	P259Q (CCA→CAA)	truA	tRNA pseudouridine(38‑40) synthase
Reads supporting (aligned to +/- strand):  ref base G (8/18);  new base T (23/0);  total (31/18)
Fisher's exact test for biased strand distribution p-value = 1.38e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAAATCGATGAGGAAATAAATCAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATA‑CA‑GCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCT  >  NC_000913/2434712‑2435009                                                                                                                                                       |                                                                                                                                                        aaaaTCGATGAGGAAATAAATCAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTgg                                                                                                                                                        <  2:370288/151‑1 (MQ=255)        aTGAGGAAATAAATCAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGGTTTTgggg                                                                                                                                                      >  1:296559/1‑145 (MQ=255)                       aGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGATTTGGAAGATCAAA‑cccggca                                                                                                                                       >  1:768572/1‑140 (MQ=255)                            cATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTTGGAGATCATA‑CCGGGCAGGGGAATCCAc                                                                                                                            >  1:307476/1‑151 (MQ=255)                            cATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTTGGAGAACATA‑CCGGTCAGGGGAATTCAc                                                                                                                            >  1:485585/1‑151 (MQ=255)                            cATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGGAGATCATA‑CCGGTCAGGGGAAAcc                                                                                                                              >  1:370417/1‑149 (MQ=255)                             atatTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTTGAAGAACAAA‑CCGGGCAGGGGAATTCAcc                                                                                                                           >  1:824424/1‑151 (MQ=255)                                 ttGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGAAGATCATA‑CCGGGCAGGGGAATCCAcc                                                                                                                           >  1:328037/1‑147 (MQ=255)                                         gCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATa                                                                                                                <  2:944530/150‑1 (MQ=255)                                          ccTTGTCCCCTTCACTTTCCAGGTTGTACCTACGTTGGCTCAAGCCTGAAAGTTCCCGGGCATTATTCCCTTTAGCCCCCCAGAAATAGCGGGCCCATT‑GC‑GGTTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATa                                                                                                                <  1:569059/148‑1 (MQ=255)                                           cTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGCTTTTGAAGAACAAA‑ACGGTCAGGGGAAAACACCCCGACCAGATA‑Ca                                                                                                             >  2:232305/1‑150 (MQ=255)                                              gTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATA‑CA‑Gcc                                                                                                         <  2:327516/150‑1 (MQ=255)                                                    gTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTTGGAGATCATA‑ACCGGCAGGGGAATTCACCGCGACCCGAAA‑CA‑ACCCtt                                                                                                      >  1:833439/1‑147 (MQ=255)                                                      cATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATA‑CA‑GCCCTTCCGCt                                                                                                 <  2:361158/150‑1 (MQ=255)                                                            tCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGGTTTTGAAGAACATA‑ACCGTCAGGGGAAGCCAACCCGACCCGAAA‑CA‑AGCCCTCCGCtttt                                                                                              >  2:448345/1‑147 (MQ=255)                                                             cAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATA‑CA‑GCCCTTCCGCTTTTGCCg                                                                                          <  2:282251/150‑1 (MQ=255)                                                               ggCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATA‑CA‑GCCCTTCCGCTTTTGCCGTtg                                                                                       <  1:706273/151‑1 (MQ=255)                                                                gCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATGGGC‑GGTTTTTGAAAATCATA‑CCGGCCCGGGGAAACCCCCCCGGCCAACAA‑CA‑GCCCCTCCCCtttt                                                                                              >  2:453092/1‑143 (MQ=255)                                                                 cTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGGAGATCATA‑CCCGGCCGGGGAAACCCCCCCGACCAGATACCA‑CCCCTTCC‑CTTTTTcc                                                                                           >  2:959262/1‑145 (MQ=255)                                                                   gTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATA‑CA‑GCCCTTCCGCTTTTGCCGTtgctg                                                                                    <  2:846466/150‑1 (MQ=255)                                                                     aaCTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTTGGAGATCATA‑ACCGGCCGGGGAATCCACCGCGACCAGATA‑CA‑GCCCTTCCGCTTTTTCCGTTTCTgcc                                                                                  >  1:209658/1‑150 (MQ=255)                                                                         aCGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATA‑CA‑GCCCTTCCGCTTTTGCCGTTGCTGCCGCCa                                                                              <  2:586648/150‑1 (MQ=255)                                                                         aCGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAACGGGCCCATTGGC‑GGTTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATA‑CA‑GCCCTTCCGCTTTTGCCGTTGCTgccgcc                                                                               <  1:933933/149‑1 (MQ=255)                                                                          cGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATA‑CA‑GCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGc                                                                            <  1:627316/151‑1 (MQ=255)                                                                           gTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATA‑CA‑GCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCg                                                                           <  2:993834/151‑1 (MQ=255)                                                                            ttGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTTGTAGATCATA‑CCCGTCAGGGGAATCCACCGCGACCAGATA‑AA‑ACCCCTCCGCTTTTTCCGGttctggcccc                                                                               >  2:515951/1‑141 (MQ=255)                                                                                 tACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTTGAAGATCATA‑CCGGGCAGGGGAAACCACCGCGACCAGATA‑CA‑ACCCTTCCCCTTTTTCCGTTGCTACCCCCCGCGTTCTGt                                                                     >  1:525189/1‑151 (MQ=255)                                                                                    aGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATA‑CA‑GCCCTTCCGCTGTTGCCGTTGCTGCCGCCAGCGTTCTGTCCt                                                                  <  2:877134/151‑1 (MQ=255)                                                                                      ccTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATA‑CA‑GCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCttt                                                                <  1:1032584/151‑1 (MQ=255)                                                                                      ccTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATA‑CA‑GCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCttt                                                                <  1:864657/151‑1 (MQ=255)                                                                                         gAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTTGAAGATCATA‑CCGGTCAGGGGAATCCACCGCGACCAGAAA‑AA‑GCCCTTCCGCCTTTTCCGTTTGTGCCCCCAGCGTTCTGTCCttt                                                                >  2:330512/1‑148 (MQ=255)                                                                                                  cGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTTGCAGATAATA‑CCCGTCACGGGAATTCACCGCGACCCCATA‑TA‑AGCCTTCCCCCTTTGCCCGTGCTGCCCCCAACGTTCTGTCCTTTTCCGCCa                                                         >  2:531815/1‑146 (MQ=255)                                                                                                    aGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGGAGATCCTA‑ACGGGCAGGGGAATCCACCGCGACCCGATA‑CA‑GCCCTTCCCCCTTTTCCGTTGCTGCCGCCAGCGGTCTGTCCCTTTTCGCCAGCAActc                                                  >  1:206801/1‑151 (MQ=255)                                                                                                     gCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGGTTTTGGAGAAAATACCCGGCCAGGGAAAT‑CACCGCGACCCAATA‑CAGGCCCTTCC‑CTTTTTCCGGTGGCGCCCCCAGCGGTCTGTTCCTTtccgccccccacac                                                  >  2:8018/1‑142 (MQ=255)                                                                                                      cATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTTGAAGATTATA‑CCCGGCCGGGGAATCCACCGCGACCAGAAA‑CA‑ACCCCTCCGCTTTTGCCGCTGCTGCCGCCCGCGGTCTGTTCTTTTccgcccgcca                                                     >  2:87784/1‑144 (MQ=255)                                                                                                      cATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTTGAAGATCATA‑CCGGTCAGGGGAATTCACCCCGACCAGATA‑AA‑ACCCTTCCGCCTTTTCCGTTGCTGCCGCCAGCGTTCTGTCCTTTTCCGCCAGCAAct                                                   >  2:807790/1‑148 (MQ=255)                                                                                                       attattCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTTGAAGATCATA‑CCCGGCAGGGGAATACACCCCCACCAGATA‑CA‑ACCCCTCCCCCTTTGCCGTTGGTGCCCCCCGCGGTTTGTTCCTTGCCCCCCGccaacc                                                  >  2:134203/1‑143 (MQ=255)                                                                                                         tattCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGAAGAACATA‑CCGGTCAAGGGAATACACCCCGACCCGGAA‑CA‑GCCCTTCCGCTTTTTGCGTTTCTGCCGCCCGCGTTCTGTCCTTTTGCGCCAGc                                                       >  1:114201/1‑141 (MQ=255)                                                                                                           ttCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTTGGAGATCATA‑CCCGTCCGGGGAATCCACCCCGACCAGATA‑AA‑GCCCCTCCGCTTTTGCCCGTGCTGCCGCCAGCGGTCTGTCCCTTGCCGCCCGCAACCCTGCt                                              >  2:1027593/1‑148 (MQ=255)                                                                                                               cGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGATTTTGGGGATCATA‑CCGGGCAGGGGAATCCACCCCGCCCAAATA‑CA‑GCCCCTCCCGTTTTTCCCCTGCTTCCCCCCACGTTCTTTTCTTTTGCGCCCCCGACACCGGTATCCAGc                                       >  2:1024616/1‑151 (MQ=255)                                                                                                                  tAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGGAGATCATA‑CCGGGCAGGGGAATCCACCGCGGCCAGATA‑CA‑GCCCCTCCGCTTTTGCCGTTGCTGCCCCCAGCGGTCTGTCCTTTTCCGCCAGCCAATCTGCTAt                                            >  1:466015/1‑143 (MQ=255)                                                                                                                     tCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTTGAAGATCATA‑CCGGTCAGGGGAATCCACCGCGACCAGATA‑CA‑GCCCCTCCGCTTTTTCCGTTGCTGCCGCCAGCGGTCTGTCCTTTGCCGCCCGCAACTCTGCTATCCAGCtctc                                   >  1:1061458/1‑149 (MQ=255)                                                                                                                      ccGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTTGAAGATCATA‑CCGGGCCGGGGAATCCACCGCGACCAGATA‑CA‑ACCCTTCCGCCTTTTCCGTTTCTGCCCCCAACGTTCTGTCCTTTGCCCCCAGCAACTCTGCTATCCCGCTCTCCgg                                >  1:980133/1‑151 (MQ=255)                                                                                                                      ccGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGAAGAACATA‑CCGGTCCGGGGAATCCACCCCGACCAGATA‑CA‑GACCCTCCGCTTTTTCCGGTGCTGCCCCCCGCGTTCTGTCCTTTTCCGCCCGCCACTCTGCTATCCAGCTCTcc                                  >  2:798854/1‑149 (MQ=255)                                                                                                                         ccAGAAATAGCGGGCCCATTGGC‑GGTTTTTGGAGATCATA‑CCGGGCAGGGGAATCCACCGCGACCAGATA‑CA‑GCCCTTTCCCTTTTTCCGTTTCTGCCCCCAGCGTTCTTTCCTTTTCCGCCCGCAACCCTGCTTTCCAGCTCTcccg                                >  1:446710/1‑146 (MQ=255)                                                                                                                         ccAGAAATAGCGGGCCCATTGGC‑GGTTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATA‑CA‑GCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTg                             <  2:432428/151‑1 (MQ=255)                                                                                                                          cAGAAATAGCGGGCCCATTGGC‑GGTTTTTGAAGATCATA‑CCGGTCAGGGGAATCCACCGCGACCAGATA‑CA‑GCCCTTCCCCTTTTTCCGTTGCTGCCGCCAGCGTTCTGTCCTTTTCCGCCCGCAACTCTGCTATCCAGCTCTCCCGCTgg                            >  1:677362/1‑151 (MQ=255)                                                                                                                           aGAAATAGCGGGCCCATTGGC‑GGTTTTTGAAGATCATA‑CCGGGCAGGGGAATCCACCGCGACCAGATA‑CA‑GCCCCTCCCCTTTTTCCGTTGCTGCCCCCCGCGTTCTGTCCTTTTCCGCCCGCAACTCTGCTATTCCGCTCTCCCGCCgg                            >  1:905333/1‑150 (MQ=255)                                                                                                                                                  gTTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATA‑CA‑GCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAg     <  2:614739/151‑1 (MQ=255)                                                                                                                                                      tGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATA‑CA‑GCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCt  <  2:592529/150‑1 (MQ=255)                                                                                                                                                      tGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATA‑CA‑GCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCt  <  1:336415/150‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                        AAAATCGATGAGGAAATAAATCAGGTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGC‑GGTTTTGGAAGATCATA‑CCGGTCAGGGTAATCCACCGCGACCAGATA‑CA‑GCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCT  >  NC_000913/2434712‑2435009

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑