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%	158.7 / NA	48	S162S (TCT→TCA)	wbbH	O‑antigen polymerase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (19/29);  total (19/29)

CTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAC  >  NC_000913_3_vch_tpiA/2106598‑2106882                                                                                                                                                |                                                                                                                                              atattatTACCGACGAGGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAATAAATTTTTTTGACCa                                                                                                                                          >  2:217872/2‑149 (MQ=255)  tATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACAAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAGGTATATTTTTTACTTACATTTGTATTAGTACATATTTGTGACCaa                                                                                                                                         >  1:44536/1‑149 (MQ=255)   aagaaCACCTAAGAAGAAAGCAAAAGAGAATAAAACCATAAAGTCAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaa                                                                                                                                        <  2:279512/146‑1 (MQ=255)           cTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAAtaaataaa                                                                                                                                <  1:603727/149‑1 (MQ=255)           cTAAGATGAATGCATAAGAGATGATAACCATAAAGACCATTTTCTTACCAGTATTCAGTATAATTTCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAAtaaataaa                                                                                                                                <  1:13388/149‑1 (MQ=255)            tACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAACCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAg                                                                                                                               >  2:282492/1‑149 (MQ=255)            tACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGAATTAGTAAATTTTTTTGACCAATAAATTAAAg                                                                                                                               >  2:38925/1‑149 (MQ=255)               gATGAATGCATAAGAGATGATAACCAAAAAGACAAGTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATTCAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCaa                                                                                                                            <  1:207439/149‑1 (MQ=255)                      atctAAAAGATGATGACCATAAAGAAAATTTGCTTACTATTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAagtagt                                                                                                                     <  1:176950/146‑1 (MQ=255)                           agagATGATGACCATAAAGACAATTTGCTTACCAGTATTAAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAAATAATAAAGCCAAAGTAATTTGat                                                                                                                >  2:176950/1‑148 (MQ=255)                           agagATGATAACCATAAAGACAATTTTTTTACCAGTATTCATTATAATTTCAAAGATTAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGaa                                                                                                                <  1:330725/149‑1 (MQ=255)                           agagATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGaa                                                                                                                <  1:340613/149‑1 (MQ=255)                             agaTGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATg                                                                                                              >  1:276576/1‑149 (MQ=255)                                  atAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTgg                                                                                                         <  1:771152/149‑1 (MQ=255)                                       cATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTGGTTAGAATGATTGGCTGCa                                                                                                    >  1:187139/1‑149 (MQ=255)                                       cATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCa                                                                                                    <  1:150114/149‑1 (MQ=255)                                             gACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATg                                                                                              >  2:783692/1‑149 (MQ=255)                                                    tccTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGaa                                                                                       <  1:691377/147‑1 (MQ=255)                                                     gCTTACCAGTATTAAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATTTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGaaa                                                                                      <  1:133143/149‑1 (MQ=255)                                                      cTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAAt                                                                                     >  1:98051/1‑149 (MQ=255)                                                                ttCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt                                                                           <  1:79459/149‑1 (MQ=255)                                                                ttCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt                                                                           >  2:675528/1‑149 (MQ=255)                                                                 tCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgtg                                                                          <  1:379759/149‑1 (MQ=255)                                                                  cAGTAAAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATgtgt                                                                         <  1:179106/149‑1 (MQ=255)                                                                   aGTATAATTGCAAAGATGAATACAATGAAAACAAGTAAAGTAAATGTTTTGCTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTc                                                                        >  1:683316/1‑149 (MQ=255)                                                                      ataATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTc                                                                     <  1:282492/149‑1 (MQ=255)                                                                            gCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATc                                                               <  1:675528/149‑1 (MQ=255)                                                                             gaaaGATGAATACAATAAGAACAAGTAAAGGAAAGTTTTTACTTACCGTTGTATTAGTAAATGTTTTTGCCCAAATAAATAAAGCAACAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCa                                                              <  2:408324/148‑1 (MQ=255)                                                                                   tGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTATATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCAtct                                                        >  1:550438/1‑149 (MQ=255)                                                                                         cAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCACATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATc                                                  <  1:194046/149‑1 (MQ=255)                                                                                         cAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATc                                                  <  1:191816/149‑1 (MQ=255)                                                                                          aaTAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCa                                                 >  2:539445/1‑149 (MQ=255)                                                                                          aaTAAAAACAAGTAAAGAAAATGTTTTACTTACCTCTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAATGTAGTTAGAATGATTGGCTGCATGTATGCTAAAAAATTTCTGGATTTGTCTCCAAGAACAGCTTCTCTTATCa                                                 >  2:339176/1‑149 (MQ=255)                                                                                           aTAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATACTGAGAAATTTCTTGATGTGTCTTCAACATCATCATCTCTTCTCaa                                                >  2:45514/1‑149 (MQ=255)                                                                                            tAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCaaa                                               >  1:224043/1‑149 (MQ=255)                                                                                                           taaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaagt                                <  2:453786/149‑1 (MQ=255)                                                                                                              aTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaa                                  >  1:701928/1‑144 (MQ=255)                                                                                                              aTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTGATCAAATTCATATAGCtaa                                  <  2:701928/144‑1 (MQ=255)                                                                                                               tGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAACTAAATAACACAAAAGTAGTTAGAATGATTGGCTGCATGTAGGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGc                            <  1:781738/149‑1 (MQ=255)                                                                                                                 ttttACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTa                          <  2:276576/149‑1 (MQ=255)                                                                                                                 gtttACTTACCTTTGTATTAGTAAATGTTTTTTACCAAATAAATAAAGCAAAAGTATTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTTATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTa                          <  2:278810/148‑1 (MQ=255)                                                                                                                              tGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGt             <  2:550438/149‑1 (MQ=255)                                                                                                                               gTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTa            <  2:224043/149‑1 (MQ=255)                                                                                                                                 aTTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGt          >  2:445596/1‑149 (MQ=255)                                                                                                                                   tAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTGGTTa        <  1:126786/149‑1 (MQ=255)                                                                                                                                    aGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTAc       <  1:71234/149‑1 (MQ=255)                                                                                                                                      tAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGCAATGGTaacaaatt     >  2:504535/1‑142 (MQ=255)                                                                                                                                         aTTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGTTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAc  <  2:44536/149‑1 (MQ=255)                                                                                                                                                |                                                                                                                                              CTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAC  >  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: ‑