Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,464,489	G→A	*317* (TAG→TAA)  D7N (GAC→AAC)	paaX → paaY →	transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer thioesterase required for phenylacetic acid degradation, trimeric, phenylacetate regulatory and detoxification protein, hexapeptide repeat protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,464,489	0	G	A	100.0%	193.2 / NA	60	*317* (TAG→TAA)  D7N (GAC→AAC)	paaX paaY	transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer thioesterase required for phenylacetic acid degradation, trimeric, phenylacetate regulatory and detoxification protein, hexapeptide repeat protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (31/29);  total (31/29)

CGCCTGCTGCTTTAGCGTTCGTTAGTGAAAAAGGTGAAACCTCGGTCGGTGAACTGCCTGCGCCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAGACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCAAGGGCGTTTACGTTGGGCCAAATGCCAGCCTGCGTGGCGATTTTGGTCGTATCGTG  >  NC_000913/1464353‑1464623                                                                                                                                         |                                                                                                                                       cgcCTGCTGCTTTAGCGTTCGTTAGTGAAAAAGGTGAAACCTCGGTCGGTGAACTGCCTGCGCCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAAc                                                                                                                                      >  2:50721/1‑139 (MQ=255)    ctgctgCTTTAGCGTTCGTTAGTGAAAAAGGTGAAACCTCGGTCGGTGAACTGCCTGCGCCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGt                                                                                                                                   <  1:66765/139‑1 (MQ=255)    ctgctgCTTTAGCGTTCGTTAGTGAAAAAGGTGAAACCTCGGTCGGTGAACTGCCTGCGCCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGt                                                                                                                                   <  1:1189862/139‑1 (MQ=255)       ctgctTTAGCGTTCGTTAGTGAAAAAGGTGAAACCTCGGTCGGTGAACTGCCTGCGCCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTg                                                                                                                                >  1:142101/1‑139 (MQ=255)          ctTTAGCGTTCGTTAGTGAAAAAGGTGAAACCTCGGTCGGTGAACTGCCTGCGCCGGGAAGCATGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACt                                                                                                                             <  2:1240163/139‑1 (MQ=255)                    cgttAGTGAAAAAGGTGAAACCTCGGTCGGTGAACTGCCTGCGCCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGc                                                                                                                   >  2:1415578/1‑139 (MQ=255)                    cgttAGTG‑AAAAGGTGAAACCTCGGTCGGTGAACTGCCTGCGCCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGcc                                                                                                                  >  2:401725/1‑139 (MQ=255)                                    gAAACCTCGGTCGGTGAACTGCCTGCGCCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGt                                                                                                   <  1:401725/139‑1 (MQ=255)                                     aaaCCTCGGTCGGTGAACTGCCTGCGCCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTc                                                                                                  <  2:32359/139‑1 (MQ=255)                                            ggtcggtGAACTGCCTGCGCCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGa                                                                                           <  1:96279/139‑1 (MQ=255)                                            ggtcggtGAACTGCCTGCGCCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGa                                                                                           <  2:175327/139‑1 (MQ=255)                                               cggtGAACTGCCTGCGCCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAg                                                                                        <  1:50721/139‑1 (MQ=255)                                                    aaCTGCCTGCGCCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTa                                                                                   <  2:1339673/139‑1 (MQ=255)                                                          ctgcGCCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTG‑ACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCg                                                                            >  1:268513/1‑139 (MQ=255)                                                            gcgcCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCgg                                                                           >  1:106555/1‑139 (MQ=255)                                                              gcCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTc                                                                                                                                  <  1:1503160/82‑1 (MQ=255)                                                              gcCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTc                                                                                                                                  >  2:1503160/1‑82 (MQ=255)                                                              gcCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCt                                                                                                                                 <  2:861661/83‑1 (MQ=255)                                                              gcCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCt                                                                                                                                 >  1:861661/1‑83 (MQ=255)                                                                   gAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGtt                                                                                                       >  2:353810/1‑104 (MQ=255)                                                                   gAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGtt                                                                                                       <  1:353810/104‑1 (MQ=255)                                                                       ccTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCa                                                                                                                 <  1:936255/90‑1 (MQ=255)                                                                       ccTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCa                                                                                                                 >  2:936255/1‑90 (MQ=255)                                                                       ccTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGc                                                                          <  2:1134636/129‑1 (MQ=255)                                                                       ccTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGc                                                                          >  1:1134636/1‑129 (MQ=255)                                                                                tCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCAAgg                                                       >  2:1678426/1‑139 (MQ=255)                                                                                     gTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCAAGGGCGtt                                                  >  2:1491690/1‑139 (MQ=255)                                                                                     gTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCAAGGGCGtt                                                  >  2:376929/1‑139 (MQ=255)                                                                                     gTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCAAGGGCGtt                                                  >  2:114308/1‑139 (MQ=255)                                                                                      ttttGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCgg                                                                           <  1:1526584/113‑1 (MQ=255)                                                                                      ttttGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCgg                                                                           >  2:1526584/1‑113 (MQ=255)                                                                                        ttGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCAAGGGCGTTTAc                                               >  2:757523/1‑139 (MQ=255)                                                                                                ttGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCAAGGGCGTTTACGTTGGGcc                                       <  1:114308/139‑1 (MQ=255)                                                                                                 tGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGa                                                                                           <  2:978578/86‑1 (MQ=255)                                                                                                 tGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGa                                                                                           >  1:978578/1‑86 (MQ=255)                                                                                                          aaCAGGAGGCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCAAGGGCGTTTACGTTGGGCCAAATGCCAGc                             >  2:544697/1‑139 (MQ=255)                                                                                                             aggaggCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCAAGGGCGTTTACGTTGGGCCAAATGCCAGCCTg                          <  1:544697/139‑1 (MQ=255)                                                                                                               gaggCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCgg                                                                           <  2:502233/88‑1 (MQ=255)                                                                                                               gaggCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCgg                                                                           >  1:502233/1‑88 (MQ=255)                                                                                                                  gCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGGGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCaa                                                         <  2:221635/103‑1 (MQ=255)                                                                                                                  gCGTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCaa                                                         >  1:221635/1‑103 (MQ=255)                                                                                                                    gTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCaa                                                         >  1:560524/1‑101 (MQ=255)                                                                                                                    gTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCaa                                                         <  2:560524/101‑1 (MQ=255)                                                                                                                    gTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCAAGGGCGTTTACGTTGGGCCAAATGCCAGCCTGCGTg                      <  1:43236/136‑1 (MQ=255)                                                                                                                    gTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCAAGGGCGTTTACGTTGGGCCAAATGCCAGCCTGCGTg                      >  2:43236/1‑136 (MQ=255)                                                                                                                    gTTATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCAAGGGCGTTTACGTTGGGCCAAATGCCAGCCTGCGTGGCg                   >  1:1189106/1‑139 (MQ=255)                                                                                                                     ttATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATg                                                                      <  2:1597764/87‑1 (MQ=255)                                                                                                                     ttATGCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATg                                                                      >  1:1597764/1‑87 (MQ=255)                                                                                                                         gCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATcc                                                                                             >  1:130686/1‑60 (MQ=255)                                                                                                                         gCCAATTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATcc                                                                                             <  2:130686/60‑1 (MQ=255)                                                                                                                             aTTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTa                                                                                   >  1:198042/1‑66 (MQ=255)                                                                                                                             aTTTATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTa                                                                                   <  2:198042/66‑1 (MQ=255)                                                                                                                              tttATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCgg                                                                           <  1:167523/73‑1 (MQ=255)                                                                                                                              tttATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCgg                                                                           >  2:167523/1‑73 (MQ=255)                                                                                                                              tttATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCAAGGGCGTTTACGTTGGGCCAAATGCCAGCCTg                          <  2:102584/122‑1 (MQ=255)                                                                                                                              tttATCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCAAGGGCGTTTACGTTGGGCCAAATGCCAGCCTg                          >  1:102584/1‑122 (MQ=255)                                                                                                                                 aTCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCAAGGGCGTTTACGTTGGGCCAAATGCCAGCCTGCGTGGCGATTTTGGTCGTAt      >  2:1229931/1‑139 (MQ=255)                                                                                                                                  tCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCgg                                                                           <  1:1320739/69‑1 (MQ=255)                                                                                                                                  tCAGATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCgg                                                                           >  2:1320739/1‑69 (MQ=255)                                                                                                                                     gATAAACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCAAGGGCGTTTACGTTGGGCCAAATGCCAGCCTGCGTGGCGATTTTGGTCGTATCgtg  <  2:142101/139‑1 (MQ=255)                                                                                                                                         |                                                                                                                                       CGCCTGCTGCTTTAGCGTTCGTTAGTGAAAAAGGTGAAACCTCGGTCGGTGAACTGCCTGCGCCGGGAAGCCTGTATTTTCAACGTTTTGGCGGCTTGAATATTGAACAGGAGGCGTTATGCCAATTTATCAGATAGACGGTCTGACTCCGGTTGTGCCAGAAGAGAGTTTTGTCCATCCGACAGCGGTATTGATCGGCGATGTTATTCTCGGCAAGGGCGTTTACGTTGGGCCAAATGCCAGCCTGCGTGGCGATTTTGGTCGTATCGTG  >  NC_000913/1464353‑1464623

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑