Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,316,160	G→A	*891* (TAG→TAA)	rcsD →	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,316,160	0	G	A	100.0%	138.9 / NA	44	*891* (TAG→TAA)	rcsD	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (22/22);  total (22/22)

TTTGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAGCAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGACTCTA  >  NC_000913/2316029‑2316291                                                                                                                                    |                                                                                                                                    tttGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTa                                                                                                                              >  1:165358/1‑139 (MQ=255) tttGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTa                                                                                                                              <  2:396964/139‑1 (MQ=255)     ccATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCt                                                                                                                          <  1:1185455/139‑1 (MQ=255)         gCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAgg                                                                                                                                <  1:81583/129‑1 (MQ=255)         gCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAgg                                                                                                                                >  2:81583/1‑129 (MQ=255)                  ggTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACaa                                                                                                             >  2:1028204/1‑139 (MQ=255)                   gTACCCGACAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAat                                                                                                            >  2:1018678/1‑139 (MQ=255)                         ggCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAAc                                                                                                      >  1:1060888/1‑139 (MQ=255)                                aGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAatta                                                                                               <  2:433543/139‑1 (MQ=255)                                 gTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAattat                                                                                              <  1:1247948/139‑1 (MQ=255)                                 gTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAattat                                                                                              <  1:523722/139‑1 (MQ=255)                                       tgAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAata                                                                                                           <  2:420963/120‑1 (MQ=255)                                       tgAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGATAGCCTATTACATGAACAata                                                                                                           >  1:420963/1‑120 (MQ=255)                                        gAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGAt                                                                                       <  1:998282/139‑1 (MQ=255)                                                       cTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATg                                                                                      <  1:467452/125‑1 (MQ=255)                                                       cTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATg                                                                                      >  2:467452/1‑125 (MQ=255)                                                                        tGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCaa                                                       >  1:1173984/1‑139 (MQ=255)                                                                         gTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCaaa                                                      >  2:1032845/1‑139 (MQ=255)                                                                                      aaaaaTACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGaa                                                                                                                >  1:224926/1‑68 (MQ=255)                                                                                      aaaaaTACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGaa                                                                                                                <  2:224926/68‑1 (MQ=255)                                                                                      aaaaaTACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCaaa                                         <  1:1028204/139‑1 (MQ=255)                                                                                             cATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGtt                                                                   <  1:399098/106‑1 (MQ=255)                                                                                             cATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGtt                                                                   >  2:399098/1‑106 (MQ=255)                                                                                              aTCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAatta                                                                                               <  1:723555/77‑1 (MQ=255)                                                                                              aTCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAatta                                                                                               >  2:723555/1‑77 (MQ=255)                                                                                              aTCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCaa                                                       >  2:1127112/1‑117 (MQ=255)                                                                                              aTCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCaa                                                       <  1:1127112/117‑1 (MQ=255)                                                                                                cAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTg                                               <  1:617695/123‑1 (MQ=255)                                                                                                cAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTg                                               >  2:617695/1‑123 (MQ=255)                                                                                                cAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGt                               >  2:422900/1‑139 (MQ=255)                                                                                                  gCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATg                                                                                                                  >  2:1422760/1‑54 (MQ=255)                                                                                                  gCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATg                                                                                                                  <  1:1422760/54‑1 (MQ=255)                                                                                                   cGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAat                                                                                                            <  2:203895/59‑1 (MQ=255)                                                                                                   cGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAat                                                                                                            >  1:203895/1‑59 (MQ=255)                                                                                                       aTTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCa                                                   <  2:1207566/112‑1 (MQ=255)                                                                                                       aTTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCa                                                   >  1:1207566/1‑112 (MQ=255)                                                                                                                    tCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGa                                                                             >  1:50849/1‑73 (MQ=255)                                                                                                                    tCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGa                                                                             <  2:50849/73‑1 (MQ=255)                                                                                                                        gagCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGa       <  1:525280/139‑1 (MQ=255)                                                                                                                         agCTTGCTGTAACAAGGTAGCCTATTACGTGAACAATATGAACGTAATTATTGCCGATGAc                                                                                    >  1:885519/1‑61 (MQ=255)                                                                                                                         agCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGAc                                                                                    <  2:885519/61‑1 (MQ=255)                                                                                                                         agCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTACGGTATTCGCAACTCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGAc      >  1:269162/1‑139 (MQ=255)                                                                                                                             tGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGACTCTa  <  2:1173984/139‑1 (MQ=255)                                                                                                                             tGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGACTCTa  >  1:694416/1‑139 (MQ=255)                                                                                                                                    |                                                                                                                                    TTTGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAGCAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGACTCTA  >  NC_000913/2316029‑2316291

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑