Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,286,965	A→G	18.0%	intergenic (+439/+101)	narI → / ← rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,286,965	0	A	G	18.0%	51.8 / 6.4	48	intergenic (+439/+101)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
Reads supporting (aligned to +/- strand):  ref base A (13/19);  new base G (5/2);  total (21/27)
Fisher's exact test for biased strand distribution p-value = 2.15e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATCCTTCCCCGCTTGGGCAGAATATTTGATTGCGGATTCGTTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCTTGAGAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGG  >  NC_000913/1286818‑1287112                                                                                                                                                    |                                                                                                                                                    cATCCTTCCCCGCTTGGGCAGAATATTTGATTGCGGATTCGTTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCg                                                                                                                                                   >  1:555057/1‑150 (MQ=255)     cTTCCCCGCTTGGGCAGAATATTTGATTGCGGATTCGTTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCg                                                                                                                                               >  1:1246240/1‑150 (MQ=255)                   cAGAATATTTGATTGCGGATTCGTTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGACGAACCTTAGt                                                                                                                                 >  2:1287681/1‑150 (MQ=255)                     taaTATGTGTTGGCGGATGAGCTTGTGTATTCGGGTTTTTTTGTTAGGGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCg                                                                                                                               <  1:1598558/149‑1 (MQ=11)                         atTTGATTGCGGATTCGTTTGAGAATTCCGGGTCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCg                                                                                                                                          <  2:1277008/135‑1 (MQ=12)                         atTTGATTGCGGATTCGTTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCg                                                                                                                                          >  1:1277008/1‑135 (MQ=21)                                  cggacgcGTTTGTCAATGCCGGGGCTTGTGTATGTGAGTGGGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATcc                                                                                                                  <  1:1068393/144‑1 (MQ=14)                                       tCGTTTGAGAATTCCGGGTCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAgtc                                                                                                                                           <  2:59309/120‑3 (MQ=255)                                       tCGTTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAgtc                                                                                                                                           >  1:59309/1‑118 (MQ=255)                                         gTTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGCCGCTCGAGACGAACCTTAGTCGAAGCTTCTCATCCTTccccc                                                                                                           >  2:555785/1‑149 (MQ=255)                                            tcagtaTTCCGGGTCTTAAGTAAGCGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCAt                                                                                                        <  1:483912/145‑1 (MQ=14)                                             gagaATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCAGCGGCAACGCTCTCTCGCTGGCGCTCGAGGCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATg                                                                                                       >  1:787508/1‑150 (MQ=255)                                               gaATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGCCGCTCGAGTCGAACCTTTGTCGAAGCTTCTCATCCTTCCCCGCATggg                                                                                                     >  1:1191192/1‑150 (MQ=255)                                                             ttGGAAGGGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGAtt                                                                                       <  2:605944/150‑1 (MQ=255)                                                             aagtaaGGGATGGTGGTGGGTGAATGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGGCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGAtt                                                                                       <  2:201697/146‑1 (MQ=14)                                                              aggaaGCGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCTCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAg                                                                                                                                  <  2:1005263/103‑1 (MQ=255)                                                              aggaaGCGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAg                                                                                                                                  >  1:1005263/4‑106 (MQ=255)                                                              aggaaGCGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCt                                                                                                                 <  1:351405/120‑1 (MQ=25)                                                              aggaaGCGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCt                                                                                                                 >  2:351405/4‑123 (MQ=25)                                                                 aaGCGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCgg                                                                                   <  1:1010282/150‑1 (MQ=255)                                                                  agggATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGa                                                                                  <  1:1609961/147‑1 (MQ=255)                                                                      ttggtggtggGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCTAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCg                                                                              <  1:1675264/149‑1 (MQ=255)                                                                      aTGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTACGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGTCGCTCTAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCg                                                                              <  1:1682663/150‑1 (MQ=255)                                                                        ggtggtggGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCt                                                                            <  1:1644797/150‑1 (MQ=40)                                                                          tggtggGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCTAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCTTg                                                                          <  1:445346/150‑1 (MQ=255)                                                                            gtggGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCTTgag                                                                        <  1:1544551/150‑1 (MQ=255)                                                                             tggGGGAAGGATTACTCAGCTCTGCGAGCTTCGACATTCGGGTCGTTGCCTGCGGCAAAGCTCTCTAGCTGACGCTAGAGCCGAACCTTAGTCGAAGCAGCTCAAACTTCCCCGCAGGGGCAGAGTATTTGAGTTCGGAGTCggtgggga                                                                       >  2:1290788/1‑143 (MQ=11)                                                                              gggtgATGGATTACTCAGCGCGGCGCGCTTCGCCCTTCGGGGCGTTGCCTGCGGCAACGCTCTCTCGCTGTCGCTCTAGGCGAACCTTTGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCTTGagag                                                                      <  2:355664/150‑1 (MQ=11)                                                                                gggAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCTTTGTCGAAGCTTCTCATCCGTCCCCGCATGGGCAGAATATTTTATTTCGGATTCGGTTGagaggg                                                                    >  2:941083/1‑148 (MQ=11)                                                                                    aGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGTCGCTCCAGTCGAACCTTTGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCTTGAGAGTTCAgg                                                                <  2:1766309/150‑1 (MQ=255)                                                                                    aGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTTGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCTTGAGAGTTCAgg                                                                <  2:1862018/150‑1 (MQ=255)                                                                                           cTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACTCTCTCTCGCTGACGCTCTAGACGAACCTTTGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCTTGAGAGTTCAGGGACtttt                                                         <  2:1668606/150‑1 (MQ=255)                                                                                            tCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCTTGAGAGTTCAGGGACTTTTg                                                        <  1:1319765/150‑1 (MQ=255)                                                                                             cAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCTGGAGAGTTCAGGGACTTTTGa                                                       >  1:1118947/1‑150 (MQ=255)                                                                                                cgcTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTTATTTCGGATTCGGTTGTGAGTTCAGGGACTTTTGAAAg                                                    >  2:564961/1‑150 (MQ=255)                                                                                                cgcTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCTTGAGAGTTCAGGGACTTTTGAAAg                                                    <  2:1012684/150‑1 (MQ=255)                                                                                                       cgctctgCCGTTCTGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGTCGCTCTAGCCGAACCTTCGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCTTGAGAGTTCAGGGACTTTTGAAAGTGAtggt                                             <  2:546868/144‑1 (MQ=14)                                                                                                       cgcTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGCCGCTCGAGGCGCGCCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGGAGAATATTTGATTGCGGATTCGGTGGTGAGTTCAGGGGCGTTTGAAAGTGAgggt                                             >  1:161974/1‑150 (MQ=11)                                                                                                         cTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCTAGTCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTg                                                                                          <  1:1003700/103‑1 (MQ=16)                                                                                                                 ttCGGGTCGTTGCCAGCGGAAACGATCTCTCGCTGAAGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCTTGGGCAGATTATATTATTGGGTATTCGATTGAGTTTTCATTTACTTTTGTAAGTGATGGTGGTGGGGGaa                                   <  2:1607428/150‑1 (MQ=14)                                                                                                                 gagagagcGTTGCCGCAGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTTATTGCGGAATCGATTGACAGTTCATGGACTTTTGAAAGTGATGGTGGTGGGGGaa                                   >  2:560708/8‑150 (MQ=14)                                                                                                                      gTCGTTGCCTGCGGCAACGCTCTCTCGCTGTCGCTCTAGTCGAACCTTCGTCGAAGCTTCTCATCCTTCCCCGCTTGGGCAGAATATTTGATTGCGGATTCGCTTGAGAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGAtt                              <  2:98708/150‑1 (MQ=11)                                                                                                                        cGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGATTGAAAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAgaaataa                            >  2:1200555/1‑144 (MQ=11)                                                                                                                         gTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGCATATTTGATTGCGGATTCGCTTGAGAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACt                           >  1:1388744/1‑150 (MQ=255)                                                                                                                             ccTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATACTTCCCCGCATGGGCAGAATATTTAATTGCGGATTAGATTGATAGTTCAGGGACTTTTTAAAGTGATGGTGGTGGGGGAAGGATTagaaccc                       >  2:362744/1‑144 (MQ=11)                                                                                                                                            tctcGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCTTGTGAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTAGACAGATCTACGAGCTTCAcc        >  2:1059688/1‑150 (MQ=14)                                                                                                                                                 cTGTCGCTCTAGTCGATCCTTTGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGTTTGCGGATTCGCTTGAGAGTTCCGGGTCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCg   <  1:1249044/150‑1 (MQ=11)                                                                                                                                                  tGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATTTTAGATTGCGGAGACGGGTGAGAGGTCAGGGCCGTTTGAAAGAGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCgg  >  1:576678/1‑150 (MQ=14)                                                                                                                                                    |                                                                                                                                                    CATCCTTCCCCGCTTGGGCAGAATATTTGATTGCGGATTCGTTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTGATTGCGGATTCGCTTGAGAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGG  >  NC_000913/1286818‑1287112

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑