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	96.8%	97.0 / ‑5.4	31	S162S (TCT→TCA)	wbbH	O‑antigen polymerase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (16/14);  minor base C (1/0);  total (17/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

TATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGG  >  NC_000913_3_pae_tpiA/2106599‑2106870                                                                                                                                               |                                                                                                                                   tATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGAAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaa                                                                                                                              >  1:128713/1‑149 (MQ=255)          cTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAAtaactaaa                                                                                                                     >  2:23633/1‑149 (MQ=255)           tACGATGAATGAATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAg                                                                                                                    <  1:260164/149‑1 (MQ=255)              gATGAATGCATAAGAGATGATAACCATAAAGACAATTCGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATACATAAAGCaa                                                                                                                 >  2:336527/1‑149 (MQ=255)                        tAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAACAAAAGTAGT‑TAg                                                                                                      >  2:367819/1‑149 (MQ=255)                           gagaTGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCACAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACTAAATAAATAAAGCAAAAGTAGT‑TAGAAt                                                                                                   >  2:480101/1‑149 (MQ=255)                                         aaaGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGt                                                                                     >  2:146464/1‑149 (MQ=255)                                            gACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATTAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATg                                                                                  <  1:307572/149‑1 (MQ=255)                                                          cAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt                                                                    >  1:162552/1‑149 (MQ=255)                                                            gTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TATAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGa                                                                  <  1:146464/149‑1 (MQ=255)                                                               ttCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCAAGTATACTGAGAAATTTCTTGAttt                                                               >  2:16079/1‑147 (MQ=255)                                                                  aGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTATTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTCCCTGTCTGCTCAGAAATTTCTTGAttcgtc                                                            >  2:158967/1‑144 (MQ=255)                                                                         ttGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAACTTTCTTGATGTGTCTTCAACa                                                     >  1:104624/1‑149 (MQ=255)                                                                            cAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATGAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCa                                                  <  1:468599/149‑1 (MQ=255)                                                                             aaaGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAg                                                 >  1:175974/1‑149 (MQ=255)                                                                                aaTGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCAt                                              <  1:406889/148‑1 (MQ=255)                                                                                 aTGAATAAAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAAAAtaactgtc                                             <  2:62672/149‑8 (MQ=255)                                                                                   gAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCAtctc                                           >  1:344814/1‑149 (MQ=255)                                                                                     aTACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTGGTATTAGTAAATTTTTTTGAGCAAATAAATAAAGC‑AAATTAGTGGAGAATGATTGGATGAATATATGCAGCAAAATTTCTTGCTGTTTCTTCACCATCAGCATCTCtt                                         >  2:377811/1‑149 (MQ=255)                                                                                       aCAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTAt                                       <  2:344814/149‑1 (MQ=255)                                                                                        cAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATc                                      <  2:175974/149‑1 (MQ=255)                                                                                        aaaTAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATc                                      <  1:174852/148‑1 (MQ=255)                                                                                                      aaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCt                        >  2:55304/1‑149 (MQ=255)                                                                                                             aTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaagtaag                 <  1:16079/149‑1 (MQ=255)                                                                                                               gTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCt               <  2:128713/149‑1 (MQ=255)                                                                                                                ttttACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTa              >  2:324067/1‑149 (MQ=255)                                                                                                                    acttacCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTcc          <  1:55304/149‑1 (MQ=255)                                                                                                                           tttGTATTAGTAAATTTTTTCGACCAATTAGATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGCAAGATATTCCCGAACTg   >  1:485047/1‑149 (MQ=255)                                                                                                                            ttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTgg  <  2:290847/149‑1 (MQ=255)                                                                                                                                     tAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATctct                                          <  2:178751/100‑1 (MQ=255)                                                                                                                                     tAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATctct                                          >  1:178751/1‑100 (MQ=255)                                                                                                                                               |                                                                                                                                   TATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGT‑TAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGG  >  NC_000913_3_pae_tpiA/2106599‑2106870

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑