Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,287,161	G→A	12.0%	noncoding (76/171 nt) Q6* (CAA→TAA)	rttR ← tpr ←	rtT sRNA, processed from tyrT transcript protamine‑like protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,287,161	0	G	A	12.0%	95.2 / 4.4	47	noncoding (76/171 nt) Q6* (CAA→TAA)	rttR tpr	rtT sRNA, processed from tyrT transcript protamine‑like protein
Reads supporting (aligned to +/- strand):  ref base G (25/13);  new base A (3/2);  total (28/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AATATTTGATTGCGGATTCGCTTGAGAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGTTGGGAAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTCGAACCTTCGAAGTCGATGACGGCAGATTTACAGTCTGCTCCCTT  >  NC_000913/1287017‑1287307                                                                                                                                                 |                                                                                                                                                   aaTATTTGATTGCGGATTCGCTTGAGAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCATCACCCTTCGGGTCGTTGCCTGAGGCAACGCTCTCTCGCTGTCGCTCGAATCGAACCTTATTCGa                                                                                                                                               >  2:653715/1‑150 (MQ=14)         aTTGCGGATTCGCTTGAGAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCGCGAGTCGAACCTTGGTCGAAGCTtctc                                                                                                                                       >  1:965803/1‑150 (MQ=255)           tGCGGATTCGTTTGAGACTTCCGGGTCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCAt                                                                                                                                     <  1:74142/150‑1 (MQ=255)            gCGGATTCGCTTGAGAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATc                                                                                                                                    >  1:673658/1‑150 (MQ=255)             cGGATTCGCTTGAGACTTCCGGGTCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATcc                                                                                                                                   <  1:802770/150‑1 (MQ=255)                aTTCGCTTGAGAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTAATCAGCGCTTCGCGCATCGCCCTTCGGTTCGTTTCCTGTGGCTACGGTCTCTCGCTTGCGCTCGAATCGAACCTTAGTAGAAGGTTCTCAAGCTTc                                                                                                                                >  1:1305329/1‑150 (MQ=14)                                     cTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTa                                                                                                           <  1:1698686/150‑1 (MQ=38)                                        ttGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGACGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGa                                                                                                                  <  1:1265088/140‑1 (MQ=21)                                          gAAAGTGATGGTGGTGGGGGAAGGATTACTCAGAGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCGGGCGCGCGAGTCGAGCCTTGGTCGAAGCTTCTCATCCTTCCACGCATGGGCGGAATATTTAATTgg                                                                                                      >  2:1873481/1‑149 (MQ=14)                                            aaGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCgg                                                                                                    <  2:974622/150‑1 (MQ=39)                                              gTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGAt                                                                                                  >  1:1036175/1‑150 (MQ=21)                                                 aTGGTGGTGGGGTAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCg                                                                                               <  1:1002228/150‑1 (MQ=37)                                                   ggtggtggGGGAAGGATTACTCAGAGCTTCGAGCTTCGCCCATCTTTTAGATGCATGAGCCAAAGCTCTCTCGCGGCCGCGAGAGTCGAAGCTAGGTAGAAGCTACTCATCCTTAACCGCATTTTCAGAATATTTAATTGCGGATTCggg                                                                                             >  2:33280/1‑148 (MQ=2)                                                      ggtggGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTTCGGATTGGTTggg                                                                                          >  2:1448538/1‑150 (MQ=255)                                                       gtggGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGTTGGGa                                                                                         <  2:673658/150‑1 (MQ=40)                                                            ggAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGCGTGGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCAGGGGCAGAATATTTAATTGCGGATTCGTTGGGAAGttg                                                                                    >  1:1033903/1‑149 (MQ=255)                                                            ggAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTa                                                                                                           >  1:682894/1‑127 (MQ=35)                                                            ggAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTa                                                                                                           <  2:682894/127‑1 (MQ=35)                                                               ccgactACGCAGCGCTGCGCGCTTCTTCTTTCGGGGCGTTGCCTGCCGCAACGCTCGAGCGGTGTCGCGAGAGCCGAAGCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGTTGGGAAGTTCAgg                                                                                 <  1:608133/145‑1 (MQ=14)                                                               aGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGTTGGGAAGTTCAgg                                                                                 <  2:1036175/150‑1 (MQ=255)                                                                ccaTTACTCAGCGCTGCGCGCTTCGCCCTTCCGGTCGCTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTCGTCGAATCTTCTCATCCTTCCCCGCTTGGGCATAATATTTAATTGCGGATTCGTTGGGAAGTTCAggg                                                                                <  2:965803/148‑1 (MQ=14)                                                                 gATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTg                                                                                                                                                    <  2:883482/81‑1 (MQ=33)                                                                 gATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGTCGAACCTTg                                                                                                                                                    >  1:883482/1‑81 (MQ=14)                                                                      cTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATGCTTCCCCGCAGGGGGAGGATATTTATTTGCGGATTCGTTGGGAAGTTCAGGGACtttt                                                                          >  1:1161775/1‑150 (MQ=17)                                                                        cAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGTTGGGAAGTTCAGGGACTTTTGa                                                                        >  2:1751527/1‑150 (MQ=255)                                                                          gcgcTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCCACGCTCTCTCGCTGGCGCTCGAGTCGAACCGTGGTCGAAGCATATCAAACTTACCCGCATGGGCAGAATATTTAATTGAGGATTAGTTGGGAAGTTGAGGGACATTTTaaa                                                                      >  2:1558836/1‑150 (MQ=17)                                                                                         cccTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTgg                                                                                                                                                   >  1:158072/1‑58 (MQ=35)                                                                                         cccTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTgg                                                                                                                                                   <  2:158072/58‑1 (MQ=35)                                                                                          ccTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGGTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTACCCCGCATGGGCAGAATTTTTAATTGGGGTTTCGTTGGGAAGTTCAGGGACTTTTCTAAGTGATGGTCGTggggg                                                      >  2:293680/1‑150 (MQ=17)                                                                                          ccTTCGGGTCGTTGCCTGCGACAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGTTGGGAAGTTCAGGGACTTTTGAAAGTGATGGTGGTggggg                                                      >  1:1212346/1‑150 (MQ=255)                                                                                           cTTCGGGTCGTTTCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCATGGTCGAAGCTTATCATACATACCCGCAAGGGCAGAATATTTAATTGCGGATTCGTTGGGAAGTTAAAGGAATTTTTAAATTGATGGTGGTGGGGGa                                                     >  2:1572846/1‑150 (MQ=17)                                                                                           cTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCTAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCgg                                                                                                    <  2:738306/103‑1 (MQ=25)                                                                                           cTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGTTGGGAAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGa                                                     >  1:1037555/1‑150 (MQ=255)                                                                                           cTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCAAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCgg                                                                                                    >  1:738306/1‑103 (MQ=17)                                                                                                ggTCGTTTCCTGCGGAAACGCTCTCTCGCTGCCGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGTTGGTAAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGAt                                                <  2:1262777/150‑1 (MQ=11)                                                                                                       gCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCCAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATACGTTCGGAAGTTCAGGGACTTTTGAAATTGATGGTGGTGGGGGAAGGATTAGAAcc                                         >  2:143002/1‑150 (MQ=17)                                                                                                         cTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCTGGGGCAGAAGATTGAAGTGCGGATGCGGTGGGGACTGCAGGGACGTTTCAAGGTGATGGAGGTGGGGGAAGGATTcttgcatt                                       >  1:783410/1‑143 (MQ=14)                                                                                                           gCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGTTGGGAAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTCGAACCTTCg                                     >  2:1647945/1‑150 (MQ=255)                                                                                                             ggCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATAGCGGATACGTTGGGAAGTTCAGGGAATTTTGAAAGTGATGGTGGTGGGTGAAGGATTCGAAACTTCGaa                                   >  2:795865/1‑150 (MQ=17)                                                                                                               cAATGCTCTCTCGATGGCGCTCTAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGTTGGTAAGTTCAGGGCCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTCGAACCTTCGAAGt                                 <  1:618839/150‑1 (MQ=17)                                                                                                                aaCGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGTTGGGAAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTCTAACCTTCGAAGTc                                >  1:1411065/1‑150 (MQ=255)                                                                                                                            cTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGTTGGGAAGTTCAggg                                                                                >  2:1119392/1‑90 (MQ=11)                                                                                                                            cTGACGCTCGAGCCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGTTGGGAAGTTCAggg                                                                                <  1:1119392/90‑1 (MQ=11)                                                                                                                                 tcTCGAGCCTAACCTTCGTCGAAGCTTCTCATCCTTCCCCGCTTGGGCAGAATATTTAATTGCGGATTCGTTGGTAAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTCGAACCTTCGAAGTCGATGACGGCAGATTTAc               <  2:479696/149‑1 (MQ=18)                                                                                                                                 gcTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGTTGGGAAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTCGAACCTTCGAAGTCGATGACGGCAGATTTAc               <  2:1212346/150‑1 (MQ=255)                                                                                                                                  cTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGTTGGGAAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTCTAACATTCGAAGTAGATGACCGCAGAGTTACa              >  1:909711/1‑150 (MQ=18)                                                                                                                                    cGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAAAATTTAATTGGGGATTCGTTGGGAAGTTAAGGGACTTTTGATAGTGATGGTGGTGGGGGAAGGATTAGAACCTTCGAAGTCCATGACGCCAGATTTACAGt            >  1:1184397/1‑150 (MQ=21)                                                                                                                                      agcttaaCCTTTTTAGAAGCTTTACATCCAGCCCGGCATTTGGAGATTATTTTATTGCGGATTCGTTTGTGATTTCCGGGTCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTCGAACCTTCGAAGTCGATGACGGCAGATTTACAGTCt          <  2:1477506/145‑1 (MQ=12)                                                                                                                                          gAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGTTGGGATGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTCGAACCTTCGAAGTCGATGACGGCAGCTTTACCGTCTGCTc      >  1:720212/1‑150 (MQ=255)                                                                                                                                             ccTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGTTGGGAAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTCGAACATTCGAAGTCGATGACGGCAGATTTACAGTCTGCTCCCt   >  1:1743128/1‑150 (MQ=255)                                                                                                                                              cTTTGTCGTAGCTTCTGATCCTTCCCCGCATGGGAAGAATATTTTATTGCGGATTCGTTGGTTAGTTCAGGGACTTTTGAAAGTGATGGTGGGGGGGGAAGGATTCGAACCTTCGAAGTCGATGACGGCAGATTTACAGTCTGCTCCCtt  <  1:1403206/150‑1 (MQ=21)                                                                                                                                                 |                                                                                                                                                   AATATTTGATTGCGGATTCGCTTGAGAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCATGGGCAGAATATTTAATTGCGGATTCGTTGGGAAGTTCAGGGACTTTTGAAAGTGATGGTGGTGGGGGAAGGATTCGAACCTTCGAAGTCGATGACGGCAGATTTACAGTCTGCTCCCTT  >  NC_000913/1287017‑1287307

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: ‑