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%	96.4 / NA	31	S162S (TCT→TCA)	wbbH	O‑antigen polymerase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (18/13);  total (18/13)

TATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACT  >  NC_000913_3_pae_tpiA/2106599‑2106868                                                                                                                                               |                                                                                                                                tATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaa                                                                                                                           >  1:269243/1‑149 (MQ=255)     aaCACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAAAAAGTAAAGTAAATGTTTTCATTACACTTGTATTAGTAAATTTTTTTGACCaaataa                                                                                                                       >  2:667822/1‑149 (MQ=255)           tACAATGGATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTATTTACCTTTTTATTAGTAAATTTTTTTGACCAAATAAATAAAg                                                                                                                 <  2:519135/149‑1 (MQ=255)              gATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCaa                                                                                                              >  1:660709/1‑149 (MQ=255)                agacagCAGAAGAGATGATAACCATAAAGACTATATGCTTACCACTATTCAGTAAAATTAAAAAAAAGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAaaaaaaaaaaaaaaaa                                                                                                            <  2:656639/144‑1 (MQ=255)                       aTAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTa                                                                                                     >  2:66008/1‑149 (MQ=255)                               tgatAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGAtt                                                                                             <  2:269243/149‑1 (MQ=255)                                   aaCCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCt                                                                                         >  2:76720/1‑149 (MQ=255)                                           aGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTAt                                                                                 <  2:660709/149‑1 (MQ=255)                                             aCAATTTGATTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGc                                                                               <  2:615930/149‑1 (MQ=255)                                                               ttCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt                                                             >  1:603324/1‑149 (MQ=255)                                                                       aaTTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCaa                                                     <  2:385885/149‑1 (MQ=255)                                                                            cAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCa                                                <  2:417137/149‑1 (MQ=255)                                                                            cAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATATTTTTGAACAAATAAATAAAGCAAACGTAGTTAGAATGATTGCCTGCATGTATGCTGAGAAATTTCTTGATGTGTATTCAACATcc                                                >  2:462169/1‑148 (MQ=255)                                                                             aaaGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAg                                               <  1:452074/149‑1 (MQ=255)                                                                               aGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCTGCa                                             >  1:190043/1‑149 (MQ=255)                                                                               aGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATATTTGGCATTGATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCa                                             >  1:421121/1‑149 (MQ=255)                                                                                       aCAATCAAAACAACAAAAGTAAATTGTTTACTTACCTTTGCATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTAt                                     <  2:216258/149‑1 (MQ=255)                                                                                          aTAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCaa                                  >  1:513116/1‑149 (MQ=255)                                                                                              aaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTc                              >  1:306194/1‑149 (MQ=255)                                                                                              aaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTc                              <  1:76720/149‑1 (MQ=255)                                                                                              aaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTCATGTGTCTTCAACATCAGCATCTCTTATCAAATTc                              <  1:66008/149‑1 (MQ=255)                                                                                                 cAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCata                           <  1:367101/149‑1 (MQ=255)                                                                                                    gtaaagtaaaTGTTTTACTTACATTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCATAAGTAGTTAGAATGATTTGCTGCATGTATGCTGAGAAATTTTTTGATGTATATTTAACATTAGCATATCGTATCAAATTCattttc                        >  2:347669/1‑145 (MQ=255)                                                                                                     taaagtaaaTGTTTTACTTACCTAAGTATTAGTAAATTTTTTTGAACAAATAAATTAACCAAAAGCAGTAAGAATGATTGGCTGCATGTATGCAGAGAAGTTTATTGATATATCTTCATATGAAGCATACCTTTTCACATTCATATAga                       >  2:116916/1‑148 (MQ=255)                                                                                                      aaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCt                      >  1:34253/1‑149 (MQ=255)                                                                                                         gtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaag                   >  1:558922/1‑149 (MQ=255)                                                                                                          taaaTGTTTTACATACCTTTGTAGAAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATACCtaagt                  >  2:431487/1‑149 (MQ=255)                                                                                                                ttttACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTa            >  1:520921/1‑149 (MQ=255)                                                                                                                  ttacttaaCTTTGGATTAGTAAATTTTTTTGAGCAAATAAATAAAGAAAAAGTAGTTAGAATGATTGGCTGTATGTATGCTGAGAAATTTCTTTATTTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAGGTAAGCTAGt          <  2:283925/149‑1 (MQ=255)                                                                                                                          cTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACt  >  1:191220/1‑149 (MQ=255)                                                                                                                                               |                                                                                                                                TATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACT  >  NC_000913_3_pae_tpiA/2106599‑2106868

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: ‑