Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	2,106,741	A→T	S162S (TCT→TCA)	wbbH ←	O‑antigen polymerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	2,106,741	0	A	T	100.0%	154.6 / NA	46	S162S (TCT→TCA)	wbbH	O‑antigen polymerase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (19/27);  total (19/27)

CTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTT  >  NC_000913_3_pae_tpiA/2106596‑2106879                                                                                                                                                   |                                                                                                                                           ctctATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGAc                                                                                                                                         <  2:186040/149‑1 (MQ=255)    tATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTCTTAG‑TAAATTTTTTTGACCaa                                                                                                                                      >  2:629345/1‑149 (MQ=255)         acacCGACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCaaataaa                                                                                                                                 <  2:545007/149‑1 (MQ=255)          cacCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCaaataaat                                                                                                                                >  1:383935/1‑149 (MQ=255)            ccTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAataaataa                                                                                                                              <  2:241795/149‑1 (MQ=255)             cTACGATGAATGCATAAGAGATGATAACCATACAGAAGAGTTCCTTATCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAAtaaataaa                                                                                                                             <  2:543940/149‑1 (MQ=255)             cTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAAtaaataaa                                                                                                                             <  2:240449/149‑1 (MQ=255)                   tgaatgaaTAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCaaaa                                                                                                                       <  1:56610/149‑1 (MQ=255)                    gAATGCATAAAAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAag                                                                                                                      <  2:424260/149‑1 (MQ=255)                       tGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTCTTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAagtag                                                                                                                   <  2:109197/149‑1 (MQ=255)                          aTAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAACGCAAAAGTAGTTa                                                                                                                >  1:22123/1‑149 (MQ=255)                           tAAGAGATGATAGCCATAAAGACAATTTGCTTAATAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACTAAATAAATAAAGTAAAAGTAGTTAg                                                                                                               >  2:428089/1‑149 (MQ=255)                               agaTGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATg                                                                                                           >  1:512189/1‑149 (MQ=255)                                 atgatAACAATAAAGAAAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACAAAATTAATAAAGCAAAAGTAGTTAGAATGAt                                                                                                         <  2:614722/149‑1 (MQ=255)                                          aTAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAg                                                                                                                            >  2:560475/1‑121 (MQ=255)                                          aTAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAg                                                                                                                            <  1:560475/121‑1 (MQ=255)                                               gACAATTTTCTTACCAGTATTCAGTATAATTGCAAACAAGAATACAATAATGACAAGTAAAGGAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATg                                                                                           <  2:196549/149‑1 (MQ=255)                                                            ccAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAGGTAAGTGTTGTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCt                                                                              <  1:606736/149‑1 (MQ=255)                                                            aaagaaTTCAATATAATATAAAAGATAAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCt                                                                              <  2:395039/144‑1 (MQ=255)                                                             cAGTATTCAGGATAAATGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt                                                                             <  1:114342/149‑1 (MQ=255)                                                                taatCAATATAATTGCAAAGATGAATACAATAAAAACAAGAAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt                                                                          <  2:595600/146‑1 (MQ=255)                                                                    cAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATgtgt                                                                      <  2:383935/149‑1 (MQ=255)                                                                     aGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAACTTTCTTCATgtgtt                                                                     >  2:282508/1‑148 (MQ=255)                                                                      gTATAGTTGCAAAGATGAATACAATAAAAACAAGTAAATTAAATGTTTTACTTACCTTTGTATTAT‑TAAATTTTCTTGATCATAGATATACAGCATAAGTCGTTAGAATGATTGCCTACACGTATGTTCAGCAATTTCTTGATGTGTCt                                                                    >  2:511568/1‑149 (MQ=255)                                                                          aaTTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTG‑CTTAGATGTATGTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCaa                                                                <  1:308551/149‑1 (MQ=255)                                                                            ttGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACa                                                              >  1:274750/1‑149 (MQ=255)                                                                            ttGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTCGTATTAG‑TAACTTATTTTGGCCAAATAAATACAGCAAAAGTAGTTAGAATGATTGACTGCATGTATGCTGGAAAATTTCTGCATGTGTCTTCAACa                                                              >  2:590077/1‑149 (MQ=255)                                                                                 aaGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTATGTATTAG‑TAAATTGTATTGACCAAAACAATAAAGCAAAAGTAGTTAGAATAATTGGCTGCAATGATTCTGAGAAATTCTTAGATGTTTCATCAActgcacc                                                         >  2:114059/1‑143 (MQ=255)                                                                                            aaTAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCa                                              >  1:204373/1‑149 (MQ=255)                                                                                             aTAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCaa                                             >  2:619140/1‑149 (MQ=255)                                                                                                  aaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCa                                        <  2:604166/149‑1 (MQ=255)                                                                                                    aaagtaaagtaAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCata                                      <  2:368926/148‑1 (MQ=255)                                                                                                     aagtaaagtaAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCatat                                     >  1:183582/1‑149 (MQ=255)                                                                                                           agtaaaTGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaa                               <  2:220297/149‑1 (MQ=255)                                                                                                            gtaaaTGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt                                                                        >  2:333388/1‑107 (MQ=255)                                                                                                            gtaaaTGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt                                                                        <  1:333388/107‑1 (MQ=255)                                                                                                                   ttttACTTACCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTa                       <  2:512189/149‑1 (MQ=255)                                                                                                                        cttacCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTATTACCTTTTTCAGTTAGCTACGTACGCCACTccc                  >  2:160266/1‑149 (MQ=255)                                                                                                                           acCTTTGTATTGG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGAt                                                                                                         <  1:293604/59‑1 (MQ=255)                                                                                                                           acCTTTGTATTAG‑TAAATTTTTTTGACCAAATACATAATGCACTATTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGaa               <  1:594518/149‑1 (MQ=255)                                                                                                                           acCTTTGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGAt                                                                                                         >  2:293604/1‑59 (MQ=255)                                                                                                                              tttGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTg            <  1:458740/149‑1 (MQ=255)                                                                                                                               ttGTATTAG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGCCCCGAACTgg           <  1:619140/149‑1 (MQ=255)                                                                                                                                      aG‑TAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTAc    <  1:113840/149‑1 (MQ=255)                                                                                                                                         tAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACtt  >  1:249047/1‑149 (MQ=255)                                                                                                                                         tAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACtt  >  1:507733/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                           CTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAG‑TAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTT  >  NC_000913_3_pae_tpiA/2106596‑2106879

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑