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%	137.1 / NA	46	S162S (TCT→TCA)	wbbH	O‑antigen polymerase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (21/25);  total (21/25)

TCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCT  >  NC_000913_3_pae_tpiA/2106597‑2106884                                                                                                                                                 |                                                                                                                                                tctATTAACACCTACGATGAATGCATAAGAGATGATAACCATACAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTCACCACTCTCGTTTTAGTAAATTTTTTTGAcc                                                                                                                                             >  2:173520/1‑149 (MQ=255)  ctATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTTACCa                                                                                                                                            >  1:74546/1‑149 (MQ=255)    aTTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaa                                                                                                                                          <  2:750675/149‑1 (MQ=255)     ttAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaat                                                                                                                                         >  2:213736/1‑149 (MQ=255)     ttAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaat                                                                                                                                         >  1:578092/1‑149 (MQ=255)        acacCGACGATGAATGCATAGGATATAATAACCATAAAGACAATTTGCTTACCATTATTCAGTATAATGGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaataaa                                                                                                                                      <  1:173520/149‑1 (MQ=255)           ccTACGATGAATGCATAAGAGATGATAAACATAAAGACAATTGGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAGAGTAAATGTTTTACTTAACTTTGTATTAGTAAATTTTTTTGATCAAataaataa                                                                                                                                   >  2:14488/1‑149 (MQ=255)            cTACGATGAATGCATAAGAGATGATAACCACAAAGACAATTTGCTTACCAATATTCAGAATCATTGCAAAACTAAATACAACACCAACAAGTAAAGTAAAGGTTTTACTTACCATTGCATTAGTCAACTTCTTTCACCAagtaattaca                                                                                                                                  >  2:24583/1‑147 (MQ=255)             tACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAg                                                                                                                                 <  1:580372/149‑1 (MQ=255)                gATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTGTAATTGCAAAGATGAATACAATACAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCACATAATTAAGGCaa                                                                                                                              >  1:241804/1‑149 (MQ=255)                  tGAATGGATTAGAAATGATAACCATAAAGAAAATATGCTTATCAGTATTCATTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTGTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCaaaa                                                                                                                            <  2:704490/149‑1 (MQ=255)                       acATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAagtagt                                                                                                                       <  2:553852/148‑1 (MQ=255)                          tAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTTACCAAATAAATAAAGCAAAAGTAGTTAg                                                                                                                    >  2:738195/1‑149 (MQ=255)                           aaGAGATGATAACCAGAAAGACAATATGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGa                                                                                                                   <  1:347669/149‑1 (MQ=255)                             gagaTGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAAt                                                                                                                 <  1:26358/149‑1 (MQ=255)                             gagaTGATAACCATAAAGACAATGTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAAt                                                                                                                 <  1:188060/149‑1 (MQ=255)                                    tatcattAAATACGATTTGTTTAGCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGc                                                                                                          <  2:421767/143‑1 (MQ=255)                                     aaCCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCt                                                                                                         <  2:578092/149‑1 (MQ=255)                                              gACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATg                                                                                                >  1:649551/1‑149 (MQ=255)                                              gACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATAGGCTGCATGTATg                                                                                                >  2:598302/1‑149 (MQ=255)                                                cAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCt                                                                                              <  2:777618/149‑1 (MQ=255)                                                  aTTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCCTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAATAGTTAGAATGATTGCCTGCATGTATGCTga                                                                                            >  2:116507/1‑149 (MQ=255)                                                      gCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGaaa                                                                                        >  2:850183/1‑149 (MQ=255)                                                            cAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt                                                                                  <  2:428415/149‑1 (MQ=255)                                                            cAGTAATCAGTATAATTTCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt                                                                                  <  1:645825/149‑1 (MQ=255)                                                               tATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt                                                                               >  1:508957/1‑149 (MQ=255)                                                               tATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt                                                                               >  1:365331/1‑149 (MQ=255)                                                                 ttCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt                                                                             >  1:114784/1‑149 (MQ=255)                                                                    aGTATAATTATATAGATATATACAATAAAAGATAGTAAAGTAATTGGTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTTGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTc                                                                          <  2:194433/149‑1 (MQ=255)                                                                          aTTGCAAAGATGAATAAAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTGAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAAc                                                                    <  2:74546/149‑1 (MQ=255)                                                                           ttGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACa                                                                   >  1:650097/1‑149 (MQ=255)                                                                            tGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTATTGATGTGTCTTCAACAt                                                                  >  1:131934/1‑149 (MQ=255)                                                                              cAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCa                                                                >  2:791150/1‑149 (MQ=255)                                                                                aaGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGc                                                              <  1:213736/149‑1 (MQ=255)                                                                                            aTAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCaa                                                  >  1:569982/1‑149 (MQ=255)                                                                                                      gtaaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAg                                        <  1:605765/149‑1 (MQ=255)                                                                                                      gtaaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAg                                        >  1:595372/1‑149 (MQ=255)                                                                                                         aagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCta                                     >  2:322081/1‑149 (MQ=255)                                                                                                          agtacaTGTTTTAATTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaa                                    <  1:830125/149‑1 (MQ=255)                                                                                                          agtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaa                                    <  1:322081/149‑1 (MQ=255)                                                                                                                tGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGc                              <  1:151297/149‑1 (MQ=255)                                                                                                                 gTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCt                             <  2:649551/149‑1 (MQ=255)                                                                                                                             tttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTg                 <  1:287987/149‑1 (MQ=255)                                                                                                                                     aGTAAATTTTTTTGACCAAATAAATAAAACAAAAATAATTATAATTATTTGCTGCATGTATGCTGATAAATTTCTTTATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTAc         <  2:44581/149‑1 (MQ=255)                                                                                                                                         aaTTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTaa     <  1:248413/149‑1 (MQ=255)                                                                                                                                          aTTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAc    <  2:724848/149‑1 (MQ=255)                                                                                                                                            ttttttGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATATCTAAGTAAGCTAGTCCCGAACTGGTAGTTATTTAACCt  >  2:744934/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                                TCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCT  >  NC_000913_3_pae_tpiA/2106597‑2106884

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: ‑