Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,106,320	G→A	*167* (TAG→TAA)	cpxP →	inhibitor of the cpx response, periplasmic adaptor protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,106,320	0	G	A	100.0%	198.1 / NA	61	*167* (TAG→TAA)	cpxP	inhibitor of the cpx response, periplasmic adaptor protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (30/31);  total (30/31)

TTAACGCCGGAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAGTAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTCCGTTATACT  >  NC_000913/4106189‑4106442                                                                                                                                    |                                                                                                                            ttAACGCCGGAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAAccc                                                                                                                      >  2:866066/1‑139 (MQ=255)         ggAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTcc                                                                                                              <  2:999004/139‑1 (MQ=255)         ggAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTcc                                                                                                              <  1:866066/139‑1 (MQ=255)         ggAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTcc                                                                                                              <  1:1251156/139‑1 (MQ=255)           agcagcAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCtt                                                                                                            >  2:1231039/1‑139 (MQ=255)                     ggTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGaca                                                                                                  <  2:193665/139‑1 (MQ=255)                     ggTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGaca                                                                                                  <  1:1231039/139‑1 (MQ=255)                              cGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTg                                                                                         <  2:491518/139‑1 (MQ=255)                               gagaAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGaca                                                                                                  <  2:109259/129‑1 (MQ=255)                               gagaAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGaca                                                                                                  >  1:109259/1‑129 (MQ=255)                                 gaAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGa                                                                                                    <  2:219056/125‑1 (MQ=255)                                 gaAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGa                                                                                                    >  1:219056/1‑125 (MQ=255)                                              cGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCt                                                                         >  1:787747/1‑139 (MQ=255)                                                            gCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑ttttttt                                                          >  1:475958/1‑139 (MQ=255)                                                               tgacgtgacgCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTcc                                                                                                              >  2:393447/1‑85 (MQ=255)                                                               tgacgtgacgCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTcc                                                                                                              <  1:393447/85‑1 (MQ=255)                                                                    tgacgCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTgg                                                                     <  2:93860/121‑1 (MQ=255)                                                                    tgacgCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTgg                                                                     >  1:93860/1‑121 (MQ=255)                                                                      acgCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAAt                                                >  2:274993/1‑139 (MQ=255)                                                                      acgCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAACAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTATCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAAt                                                >  1:957423/1‑139 (MQ=255)                                                                       cgCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAAtt                                               >  1:776564/1‑139 (MQ=255)                                                                             ggCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTCTCCTCAATTTGCctg                                         <  2:957423/139‑1 (MQ=255)                                                                             ggCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCctg                                         <  1:274993/139‑1 (MQ=255)                                                                                  aaaaGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCtg                                                                        <  1:732175/104‑1 (MQ=255)                                                                                  aaaaGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCtg                                                                        >  2:732175/1‑104 (MQ=255)                                                                                  aaaaGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTgctgct                                    <  2:787747/139‑1 (MQ=255)                                                                                    aaGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCa                                                                                                        >  1:434347/1‑70 (MQ=255)                                                                                    aaGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCa                                                                                                        <  2:434347/70‑1 (MQ=255)                                                                                        tCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATcc                                                                                            >  1:919551/1‑78 (MQ=255)                                                                                        tCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATcc                                                                                            <  2:919551/78‑1 (MQ=255)                                                                                        tCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCctg                                         >  1:723378/1‑128 (MQ=255)                                                                                        tCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCctg                                         <  2:723378/128‑1 (MQ=255)                                                                                        tCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTgctgct                                    >  2:172502/1‑133 (MQ=255)                                                                                        tCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTgctgct                                    <  1:172502/133‑1 (MQ=255)                                                                                        tCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGc                              >  1:477284/1‑139 (MQ=255)                                                                                        tCATCGTTGAAGCTATTGAGTAGTAGCAACACACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGc                              >  1:1292887/1‑139 (MQ=255)                                                                                                      aTTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTgctgct                                    >  1:490390/1‑119 (MQ=255)                                                                                                      aTTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTgctgct                                    <  2:490390/119‑1 (MQ=255)                                                                                                       ttGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTg               >  2:672845/1‑139 (MQ=255)                                                                                                        tGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGc              <  1:948417/139‑1 (MQ=255)                                                                                                        tGAGTAGTAGCAACACACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGc              <  2:1292887/139‑1 (MQ=255)                                                                                                         gAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCt             <  1:454565/139‑1 (MQ=255)                                                                                                               tagCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATc                                                      >  1:634772/1‑92 (MQ=255)                                                                                                               tagCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATc                                                      <  2:634772/92‑1 (MQ=255)                                                                                                                 gCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCcaca                                                                             >  2:616242/1‑68 (MQ=255)                                                                                                                 gCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCcaca                                                                             <  1:616242/68‑1 (MQ=255)                                                                                                                 gCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTCCGTtat     >  2:375862/1‑139 (MQ=255)                                                                                                                   aaCTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTCCGTtata    <  2:475958/139‑1 (MQ=255)                                                                                                                    aCTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCctg                                         <  2:1236507/100‑1 (MQ=255)                                                                                                                    aCTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCctg                                         >  1:1236507/1‑100 (MQ=255)                                                                                                                    aCTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCctg                                         <  2:715668/100‑1 (MQ=255)                                                                                                                    aCTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCctg                                         >  1:715668/1‑100 (MQ=255)                                                                                                                    aCTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCtt            <  1:1037540/129‑1 (MQ=255)                                                                                                                    aCTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCtt            >  2:1037540/1‑129 (MQ=255)                                                                                                                    aCTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTCCGTTATACt  >  2:544652/1‑139 (MQ=255)                                                                                                                         cGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATc                                                      >  1:921217/1‑82 (MQ=255)                                                                                                                         cGTTCCAAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTAATc                                                      <  2:921217/82‑1 (MQ=255)                                                                                                                          gTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCca                                                                               >  2:1025023/1‑57 (MQ=255)                                                                                                                          gTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCca                                                                               <  1:1025023/57‑1 (MQ=255)                                                                                                                          gTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCctg                                         >  2:388137/1‑94 (MQ=255)                                                                                                                          gTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCctg                                         <  1:388137/94‑1 (MQ=255)                                                                                                                                    |                                                                                                                            TTAACGCCGGAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAGTAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTCCGTTATACT  >  NC_000913/4106189‑4106442

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑