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%	124.2 / NA	37	S162S (TCT→TCA)	wbbH	O‑antigen polymerase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (20/17);  total (20/17)

TTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCTCA  >  NC_000913_3_vch_tpiA/2106601‑2106886                                                                                                                                             |                                                                                                                                                  ttAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCCGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaat                                                                                                                                           >  1:479846/1‑149 (MQ=255)      acCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATAAAATTTAAGCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAaataaata                                                                                                                                      >  1:157711/1‑149 (MQ=255)        cTACGATGAATGCATAAGAGATGATAACCATAACGCCCATTTGCTCACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTGACCTTTGTATGAGTAAATTTTTTTGACCAAAtaaataaa                                                                                                                                    >  2:533825/1‑149 (MQ=255)        cTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAAtaaataaa                                                                                                                                    >  1:75068/1‑149 (MQ=255)          aCGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTGTCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGc                                                                                                                                  >  1:671953/1‑149 (MQ=255)              tGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCaaaa                                                                                                                              <  2:370903/149‑1 (MQ=255)                 aTGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAagta                                                                                                                           >  1:167191/1‑149 (MQ=255)                    cATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTAATTCAAGGAAGAGAAGTACATTTTTTTGACCAAATAAATAAAGCAAAAGTAGtt                                                                                                                        >  1:492499/1‑149 (MQ=255)                         gatatgatAACCATAAAGTAAATTTGATTACTATTATTCAGTATAAGTGCAAAGATTAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAAt                                                                                                                   <  2:19613/146‑1 (MQ=255)                               atAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTgg                                                                                                             <  1:420716/149‑1 (MQ=255)                                tAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGc                                                                                                            <  1:114302/149‑1 (MQ=255)                                     aTAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGTTCAAATTAATAAAGCAAAAGTAGATAGAATGATTCGCTGCAt                                                                                                       >  2:447993/1‑149 (MQ=255)                                          gACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATg                                                                                                  <  2:127848/149‑1 (MQ=255)                                                ttGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTGGTTAGAATGATTGGCTGCATGTATGCTgaga                                                                                            >  1:616/1‑149 (MQ=255)                                                    ttACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACATACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAAtt                                                                                        >  1:586316/1‑149 (MQ=255)                                                    ttACCAGTATTCAGTATAATTACAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAAtt                                                                                        >  1:543715/1‑149 (MQ=255)                                                        cAGTAATCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGCGAAATTTCtt                                                                                    >  2:626463/1‑149 (MQ=255)                                                          gTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGa                                                                                  >  2:130198/1‑149 (MQ=255)                                                           tATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGACTGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt                                                                                 <  2:589713/149‑1 (MQ=255)                                                           tATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTACCACCGCTGGGCGGCATGTATGCTGAGAAATTTCTTCAt                                                                                 >  1:186555/1‑149 (MQ=255)                                                             ttCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt                                                                               >  1:604283/1‑149 (MQ=255)                                                             ttCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTAAttt                                                                               >  2:572357/1‑147 (MQ=255)                                                                aGTATAGTTGGAAAGATTAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAATTAAAGCAAAAGTAGTTAGAAGGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTc                                                                            <  2:212715/149‑1 (MQ=255)                                                                 gTATAATTGGAAAGATGAATAAAAGAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCt                                                                           <  2:239277/149‑1 (MQ=255)                                                                          cAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCa                                                                  <  1:267403/149‑1 (MQ=255)                                                                                       aaTAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAACAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCa                                                     >  2:109595/1‑149 (MQ=255)                                                                                                  gtaaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAg                                          >  1:151113/1‑149 (MQ=255)                                                                                                      agtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaa                                      <  2:543715/149‑1 (MQ=255)                                                                                                              ttttACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtg                                                                                >  2:496070/1‑99 (MQ=255)                                                                                                              ttttACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtg                                                                                <  1:496070/99‑1 (MQ=255)                                                                                                                      acCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATAAGCATGTGTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGaa                      <  1:533825/149‑1 (MQ=255)                                                                                                                      acCTTTGTATTAGGAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGaa                      <  2:236072/149‑1 (MQ=255)                                                                                                                        cTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCCGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACt                    >  1:270735/1‑149 (MQ=255)                                                                                                                         tttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTg                   <  2:157711/149‑1 (MQ=255)                                                                                                                          ttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTgg                  <  2:17824/149‑1 (MQ=255)                                                                                                                          tggTATTAGTAAATTTTTTTGACCAAATAAAGAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCGTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTgg                  <  2:17826/147‑1 (MQ=255)                                                                                                                                 aggaaaTTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTAc           <  2:186555/146‑1 (MQ=255)                                                                                                                                          ttttGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCCTGTATGCTCAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCTCa  <  1:190000/149‑1 (MQ=255)                                                                                                                                             |                                                                                                                                                  TTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCTCA  >  NC_000913_3_vch_tpiA/2106601‑2106886

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: ‑