Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_vch_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_vch_tpiA	2,106,741	0	A	T	100.0%	175.5 / NA	51	S162S (TCT→TCA)	wbbH	O‑antigen polymerase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (31/20);  total (31/20)

CTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAC  >  NC_000913_3_vch_tpiA/2106598‑2106882                                                                                                                                                 |                                                                                                                                              ctATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGGATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGATCa                                                                                                                                          >  1:54749/1‑149 (MQ=255)    ttAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTATATTAGTAAATTTTTTTGACCaaat                                                                                                                                       >  2:360554/1‑149 (MQ=255)            tACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTATCTTTGTATTATTAAATTTTTTTCACCATATAAATTAAg                                                                                                                               >  2:355680/1‑149 (MQ=255)            tACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAg                                                                                                                               >  1:645745/1‑149 (MQ=255)               gATGAATGCATAAGAGATGATAAACATAAAGACAATTTGCTTACCAGTATTCAGTAGAGTTGCAAAGATTGAGACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGAATTAGTAACTTTTTTTGACCAAATAAATAAAggag                                                                                                                            >  2:602179/1‑146 (MQ=255)                    aTGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAagta                                                                                                                       >  1:814021/1‑149 (MQ=255)                     tGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAagtag                                                                                                                      >  1:307130/1‑149 (MQ=255)                       cATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGtt                                                                                                                    <  1:447050/149‑1 (MQ=255)                        aTAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTa                                                                                                                   <  1:396142/149‑1 (MQ=255)                                           aaGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTa                                                                                                >  1:361951/1‑149 (MQ=255)                                           aaGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTa                                                                                                >  1:392633/1‑149 (MQ=255)                                            aGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATTATTGGCTGCATGTAt                                                                                               >  2:424057/1‑149 (MQ=255)                                               cAATTTGCTTACAAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCt                                                                                            <  2:132043/149‑1 (MQ=255)                                                           cAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt                                                                                <  1:316135/149‑1 (MQ=255)                                                           cAGTATTCAGTACAATTGCAAAAACGAATACAAAAAAAATAACTCCAGCCAGACGATTT‑CCGACCTTTGTACTAGTAACAATTTGTCACCAAAGAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt                                                                                <  2:809117/149‑1 (MQ=255)                                                             gTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGa                                                                              <  2:626977/149‑1 (MQ=255)                                                             gTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGa                                                                              <  1:325570/149‑1 (MQ=255)                                                             gTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTAACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATACTGATAGATTTCttca                                                                              >  2:409578/1‑147 (MQ=255)                                                              tATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt                                                                             >  1:682353/1‑149 (MQ=255)                                                                   aGTATAATTGCAAAGATGAATACAATAAAAACACGTAAAG‑TTAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTc                                                                        >  1:625517/1‑149 (MQ=255)                                                                    gTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTTAATTTTTTTAACCAAATAAATAAAGCAAAAGTGATTAGAATGATTGGCTGCATGTATGCTGGGAAATTTCTTGATGTGTCt                                                                       >  1:808906/1‑149 (MQ=255)                                                                    gTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTCGTGATAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCt                                                                       >  2:633277/1‑149 (MQ=255)                                                                          ttGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACa                                                                 >  1:275776/1‑149 (MQ=255)                                                                             cAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTga                                                                                          <  2:799133/121‑1 (MQ=255)                                                                             cAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTga                                                                                          >  1:799133/1‑121 (MQ=255)                                                                              acaGATGCCTACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTTTCTTCAACATCAg                                                             >  2:144164/3‑149 (MQ=255)                                                                              aaaGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAg                                                             >  1:358126/1‑149 (MQ=255)                                                                                  aTGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCAtc                                                         <  1:228916/149‑1 (MQ=255)                                                                                   tGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTTGATTGAATTATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCAtct                                                        <  1:410761/149‑1 (MQ=255)                                                                                     aaTACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTTTTTTTTTTTATAACATAAAAGTAGATAGAATTATTGGCTGTATGTCTGCTGAGAAATTACTTGATGTTCCTTCACCATTACCATcact                                                      >  2:644784/1‑149 (MQ=255)                                                                                            tAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCaaa                                               >  1:684944/1‑149 (MQ=255)                                                                                               gaataagtaaag‑gaAATGTTTTAATTACCTGTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTc                                            <  2:35870/145‑1 (MQ=255)                                                                                                   aagtaaag‑taAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCatat                                        >  2:796849/1‑149 (MQ=255)                                                                                                   aagtaaag‑taAATGTTTTACTTACCTTTGTATTAGCAAATGTTGTTGACCAAATAAATAAAGCAAGAGTAGTTAAAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTATCTTCAACATCAGCATCTCTTGTCAAATTCatat                                        >  2:355909/1‑149 (MQ=255)                                                                                                       aaag‑taaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATATATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAGTTTGTTGATGTGTCTTCCACATTATCATTTGTTATCAAATTCATCTAACt                                    >  2:767030/1‑149 (MQ=255)                                                                                                         ag‑taaaTGTTGTACTTACCTTTGTATTAGTAAATTTTTGTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaa                                  <  2:71754/149‑1 (MQ=255)                                                                                                          g‑taaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaag                                 >  1:839345/1‑149 (MQ=255)                                                                                                             aaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaagta                               >  1:731686/1‑149 (MQ=255)                                                                                                              aaggTTTTACTTATCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaagtaa                              <  2:20881/146‑1 (MQ=255)                                                                                                                  ttttACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTa                          >  1:234750/1‑149 (MQ=255)                                                                                                                            cTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCCAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCCGCATCTCTTATCAAATTCATATACCTAAGTAAGCTATTACCGAACt                >  2:290578/1‑149 (MQ=255)                                                                                                                            cTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAGCt                >  1:450/1‑149 (MQ=255)                                                                                                                            cTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACt                <  2:756029/149‑1 (MQ=255)                                                                                                                              ttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTgg              <  1:370499/149‑1 (MQ=255)                                                                                                                              ttGTAGTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTgg              <  1:782577/149‑1 (MQ=255)                                                                                                                                     aGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTACGCTAGTCCCCAACTGGTAGTTAc       <  2:710376/149‑1 (MQ=255)                                                                                                                                     aGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTAc       <  2:675864/149‑1 (MQ=255)                                                                                                                                       tAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCat                                          >  2:717012/1‑112 (MQ=255)                                                                                                                                       tAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCat                                          <  1:717012/112‑1 (MQ=255)                                                                                                                                       tAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTGGTCCCGAACTGGTAGTTGCtt     >  1:401195/1‑149 (MQ=255)                                                                                                                                          aTTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAc  <  2:623274/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                              CTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAG‑TAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAC  >  NC_000913_3_vch_tpiA/2106598‑2106882

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: ‑