Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,537,068	A→G	17.9%	intergenic (+45/+58)	nadE → / ← PP_4870	NH(3)‑dependent NAD(+) synthetase/azurin

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,537,068	0	A	G	17.9%	121.5 / 19.3	56	intergenic (+45/+58)	nadE/PP_4870	NH(3)‑dependent NAD(+) synthetase/azurin
Reads supporting (aligned to +/- strand):  ref base A (24/22);  new base G (4/6);  total (28/28)
Fisher's exact test for biased strand distribution p-value = 7.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.39e-01

TTCCTGCATGGGCAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGTCACCACCGGCTTCCAGCTTG  >  NC_002947/5536925‑5537213                                                                                                                                                |                                                                                                                                                    ttCCTGCATGGGCAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTACCCCGCGAAAAAGAGGGTGAACCCAc                                                                                                                                                >  2:114726/1‑149 (MQ=255)   ccTGCATGGGCAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCAcc                                                                                                                                               >  7:312759/1‑148 (MQ=255)     tGCATGGGCAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTGACCCGCGGAAAAGCCGGTGAACCCACCGAc                                                                                                                                            >  3:62607/1‑149 (MQ=255)          ggacAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCGCCCGCGAATACGAGGGTGAACCCACCGACGCAt                                                                                                                                        >  6:349888/4‑148 (MQ=255)           ggCAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTc                                                                                                                                      >  2:247546/1‑149 (MQ=255)              aGCCGGTTGACCAGGCTGCGTTCGACATCATCGTCGCCACGTCCCGCAAGACCCTGCACAAGCGCGAACTGCCGTTCGCTCATTCATAAGTGGCCTGCAGCAGCGGTTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTcgcg                                                                                                                                   <  8:17087/149‑1 (MQ=255)               gccgcctGACCCGCCAGCGCTCGACATCACCCCCGCCCCCCACCGCACCACCCCCCACCCCCGCCACCTGCCGCTCGCTCCTTCATACGTGCCCTGCAGCAGCGGGTCCCCCCGCGAATACGAGGCTGAACCCACCGACGCATTCGCgg                                                                                                                                  <  8:312759/143‑1 (MQ=255)               gCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATGCGTCGGTGGGTTCACCCTCGTATTCGCgg                                                                                                                                  <  8:40225/149‑1 (MQ=25)               gCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATGCGTCGGTGGGTTCACCCTCGTATTCGCgg                                                                                                                                  <  6:184564/149‑1 (MQ=25)               gCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCgg                                                                                                                                  <  1:339428/149‑1 (MQ=255)               gCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAACTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCgg                                                                                                                                  <  6:210111/149‑1 (MQ=255)                 cGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGt                                                                                                                                <  1:247546/149‑1 (MQ=255)                 cGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGt                                                                                                                                <  7:6891/149‑1 (MQ=255)                         cAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATGCGTCGGTGGGTTCACCCTCGTATTCGCgg                                                                                                                                  <  8:293970/139‑1 (MQ=21)                         cAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATGCGTCGGTGGGTTCACCCTCGTATTCGCgg                                                                                                                                  >  7:293970/1‑139 (MQ=21)                                                     ccTACCGCAATACCCAGCACAAGCGCTAACTGCCTTTCGCTCCTTGATATGTGGCCTGCTGGAGCGGGTTCCCCCGCTAATACGCGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGa                                                                                            <  1:114726/149‑1 (MQ=38)                                                      cTACCGCAAGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTAACCCGCGAATACGAGGGTGTACCCACCGACGCATTAGCGGGTGAAACCGCTCCGGCAGGGGTCGCCGGCAGCCTTTGAt                                                                                           >  1:100012/1‑149 (MQ=255)                                                        aCCGCAAGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCa                                                                                                    <  3:94060/138‑1 (MQ=255)                                                          cGCAAGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACt                                                                                       >  3:240886/1‑149 (MQ=255)                                                             aaGACCCACCAAACGCGCTAACTGCGGTTGGCTCTTTTATAAGTGGCTTGCAGGAGGGGGTTCACCCGCTAATACGTGGGTTAACCCACGGACGCTTTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGa                                                                                    <  6:120213/149‑1 (MQ=255)                                                              aGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATGCGTCGGTGGGTTCACCCTCGTATTCGCgg                                                                                                                                  <  1:192921/102‑1 (MQ=14)                                                              aGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATGCGTCGGTGGGTTCACCCTCGTATTCGCgg                                                                                                                                  >  2:187165/1‑102 (MQ=14)                                                              aGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATGCGTCGGTGGGTTCACCCTCGTATTCGCgg                                                                                                                                  >  2:192921/1‑102 (MQ=14)                                                              aGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATGCGCCGGTGGGTTCACCCTCGTATTCGCgg                                                                                                                                  <  1:187165/102‑1 (MQ=17)                                                                  ccAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATGCGTCGGTGGGTTCACCCTCGTATTCGCgg                                                                                                                                  >  6:155747/1‑98 (MQ=14)                                                                  ccAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATGCGTCGGTGGGTTCACCCTCGTATTCGCgg                                                                                                                                  <  5:155747/98‑1 (MQ=14)                                                                   cAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTAACCCCCCAATACACGGGTGCACCCACCGACGCATTCGCGGGTGAACCCCCTACTGGAGGGTTGCCACTCAGCCGATGAATACTAGaagcaga                                                                              >  2:291752/1‑143 (MQ=255)                                                                    aGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGTGGGTg                                                                                                                               >  8:18906/1‑99 (MQ=255)                                                                    aGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGTGGGTg                                                                                                                               <  7:18906/99‑1 (MQ=255)                                                                       acaAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCtt                                                                        <  5:349888/149‑1 (MQ=255)                                                                       acaAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTAAACCGCGAAAAAGAGGGTGAAACCACCCACCCAATCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTGAGCCGTTGATTACTTTACGAT‑‑GAACtt                                                                        >  4:212607/1‑149 (MQ=255)                                                                         aaGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGGGGGTGAACCCCCCGCCGCATTAGCGGGTGAACCCGCGCCTGGAGGGTTCGCCGGCCGCCTTTGATTACTTGAGGAT‑‑GACCTTgg                                                                      >  5:127438/1‑148 (MQ=255)                                                                            cgcgAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGc                                                                                                                        <  8:251529/98‑1 (MQ=255)                                                                            cgcgAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGc                                                                                                                        >  7:251529/1‑98 (MQ=255)                                                                                 aCTGCCGTTCCCTCCTTGATAAGGGGCCTCCCGGAGCGGGTTCCCCCGCGAATACGAGGGGGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTtcatc                                                              <  6:127438/149‑1 (MQ=38)                                                                                     ccGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTTAACCAACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCg                                                          <  7:316159/149‑1 (MQ=255)                                                                                           gCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCTAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGAt                                                                                           <  7:159944/112‑1 (MQ=255)                                                                                                    tAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATAAGAGGGTGAACCCACCGCCGCATTCGCGGGTGAACCCGCGCCGGGAGGGGTGGGCGGCAGCCGTTTATTACTTGACGAA‑‑GGCCGTGGCATTCATCATGGAGATTGGGCCCggg                                            >  4:264725/1‑148 (MQ=19)                                                                                                       gTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAgg                                        <  4:240886/149‑1 (MQ=255)                                                                                                         ggCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTg                                      <  7:216306/149‑1 (MQ=255)                                                                                                           catGCAGTAGCGGGTTCACCCGCTAATACGAGGGTGAACCCACCGACGCATTCGCGGGTTAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCa                                    <  3:212607/147‑1 (MQ=255)                                                                                                                aGGAGCGGGTTAACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCagaag                                >  2:111081/1‑148 (MQ=255)                                                                                                                  gAGCGGGTTCACCCGCGAATACGAGGTGGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGaagaag                             <  2:100012/149‑1 (MQ=255)                                                                                                                  gAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGaagaag                             >  5:74628/1‑149 (MQ=255)                                                                                                                      gggTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTg                          >  6:246180/1‑148 (MQ=255)                                                                                                                        gTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAg                       >  1:302232/1‑149 (MQ=255)                                                                                                                         ttCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGt                      >  1:281283/1‑149 (MQ=255)                                                                                                                          tCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGt                      >  5:268728/1‑148 (MQ=255)                                                                                                                            aCCCGCTAATCCGCGGGCCAACCCACCCCCGCATGCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGTcac                   <  4:196166/149‑1 (MQ=255)                                                                                                                             cccGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGTcac                   >  7:237250/1‑148 (MQ=255)                                                                                                                              ccGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGTcacca                 >  4:69580/1‑149 (MQ=255)                                                                                                                               cgcgAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGTcaccac                >  2:324475/1‑149 (MQ=255)                                                                                                                                        gAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCa                                    >  2:138321/1‑120 (MQ=255)                                                                                                                                        gAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCa                                    <  1:138321/120‑1 (MQ=255)                                                                                                                                          gggTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGTCACCACCGGCTTCCAGc     <  3:69580/149‑1 (MQ=255)                                                                                                                                            gTGAACCCACCGACGCATTCGCGGGTGGACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGTCACCACCGGCTTCCAGCtt   >  7:129589/1‑149 (MQ=255)                                                                                                                                                aCCCACCGACTCTTTCGCGGGGTAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGTATTCTTGTCGATTCTATTTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGTCACCACCGGCTTCCAGCTTg  <  1:291752/148‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                    TTCCTGCATGGGCAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCGCGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCGGGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGAT‑‑GACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGTCACCACCGGCTTCCAGCTTG  >  NC_002947/5536925‑5537213

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: ‑