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	98.2%	181.3 / NA	56	S162S (TCT→TCA)	wbbH	O‑antigen polymerase
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base T (27/28);  total (27/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCTCA  >  NC_000913_3_pae_tpiA/2106596‑2106886                                                                                                                                                  |                                                                                                                                                  ctctATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGAc                                                                                                                                                <  2:401325/149‑1 (MQ=255)     aTTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTCTTTTGCGTTGTATTAGTAAATTTTTTTGACCaaa                                                                                                                                            <  2:659687/149‑1 (MQ=255)           acCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAaataaata                                                                                                                                      >  1:343860/1‑149 (MQ=255)            ccTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAataaataa                                                                                                                                     >  1:34709/1‑149 (MQ=255)             cTACGATGAATGCATAATAGATGCTAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAAGAAGTAAAGTAAATGTTTTACTTACCCTTGTATTAGTAAATTTTTTTGACCAAAtaaataaa                                                                                                                                    <  1:575491/149‑1 (MQ=255)             cTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAAGAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAAtaaataaa                                                                                                                                    >  2:589995/1‑149 (MQ=255)             cTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTACTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAAtaaataaa                                                                                                                                    >  2:461077/1‑149 (MQ=255)             cTACGATGAAGACATAAGGGAAGATAAACATAAAGACAATTTGCTTCTTAGTATTCAGTATAATTTCAAATACAAACAGAATAAAAACAACTAAAGTAAATGTTTTACTTATCTTTGTATTAGTAAATTTTTTTGACCAAAtaaataaa                                                                                                                                    <  2:167923/149‑1 (MQ=255)                 gATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGCAGTCAGAAGGATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCaa                                                                                                                                >  2:286806/1‑149 (MQ=255)                      aTGCTTAATAGATGACACCCATAAGGACTAGGTGCTTACCAGTATTCAGTATAATTGCAAAGATTAATACAATAAATACAAGTAAAATAAATGTTCTAATTACTTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAagta                                                                                                                           <  2:407814/149‑1 (MQ=255)                      aTGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAagta                                                                                                                           >  1:48393/1‑149 (MQ=255)                        gCATAAGAGATGATAACTACAAAGACAATTTGCTTACCAGTATTCAATATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAAATTTTTTGACCAGATAAATAAAGCAAAagtagt                                                                                                                         <  2:251691/149‑1 (MQ=255)                             agagATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaataaat                                                                                                                                       >  2:527475/1‑130 (MQ=255)                             agagATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaataaat                                                                                                                                       <  1:527475/130‑1 (MQ=255)                              gagaTGATAACCATAAAGACAATTTGCTTACCAGAATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTCGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAAt                                                                                                                   >  2:541537/1‑149 (MQ=255)                                    atAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTgg                                                                                                             <  1:583860/149‑1 (MQ=255)                                         cATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAAAAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAATAGTAGTTAGAATGATTGGCTGCa                                                                                                        >  2:346611/1‑149 (MQ=255)                                          aaaaaTACAATTTTCTTACCAGTATTTAGTATAATTACAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCAt                                                                                                       <  1:99251/147‑1 (MQ=255)                                          aTAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGATTGATTGGCTGCAt                                                                                                       >  1:268879/1‑149 (MQ=255)                                             aaGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTa                                                                                                    <  1:635844/149‑1 (MQ=255)                                                aCAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGc                                                                                                 <  1:322583/149‑1 (MQ=255)                                                  aaTTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTg                                                                                               >  2:329901/1‑149 (MQ=255)                                                       gCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTAt                                                                                                   <  2:419885/140‑1 (MQ=255)                                                       gCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTAt                                                                                                   >  1:419885/1‑140 (MQ=255)                                                           aCCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTTTTTTTTTTTTTAACGCAAAAGTAGTTAGAATAATTGTTCGCATGAATGCAAAGAAATTTc                                                                                      >  2:513714/1‑149 (MQ=255)                                                                  ttCAGTATAATTGCAAAGATAAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt                                                                               <  1:411413/149‑1 (MQ=255)                                                                     aGTATAATTTTAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGACAAATTTCTTGATGTGTc                                                                            >  2:98633/1‑149 (MQ=255)                                                                     aGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTc                                                                            >  1:414601/1‑149 (MQ=255)                                                                        ataATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTc                                                                         >  1:667439/1‑149 (MQ=255)                                                                          aaTTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCaa                                                                       >  1:483771/1‑149 (MQ=255)                                                                                   gATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCAt                                                              <  2:483771/149‑1 (MQ=255)                                                                                            aaTAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTGAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCa                                                     >  2:591548/1‑149 (MQ=255)                                                                                                aaaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAAtt                                                 <  2:269997/149‑1 (MQ=255)                                                                                                 aaaCAAGTAAATTAAATATTTGTCTGACTTTTGTATTAGTAAATTTTTTTCACCAAAAAAAAAAAACAAAAGTAGTTATAATGATTGGCTGGATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTc                                                <  2:242282/149‑1 (MQ=255)                                                                                                 aaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTGTTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTc                                                >  1:35050/1‑149 (MQ=255)                                                                                                 aaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt                                                                                    >  1:177481/1‑113 (MQ=255)                                                                                                 aaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt                                                                                    <  2:177481/113‑1 (MQ=255)                                                                                                           agtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaa                                      <  1:499598/149‑1 (MQ=255)                                                                                                             taaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaagt                                    >  1:597520/1‑149 (MQ=255)                                                                                                             taaaTGTTATACTCACCTTTGTATTAGTAAATTTTTTTGATCAAATAAATAAAGAAAAAGTAGTTAGAATGATTGGCTGCCTGTATGCTGAGAAATCTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaagt                                    <  2:668657/149‑1 (MQ=255)                                                                                                              aaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTga                                                                                              <  2:435892/90‑1 (MQ=255)                                                                                                              aaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTga                                                                                              >  1:435892/1‑90 (MQ=255)                                                                                                                   ttttACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCa                                                                  >  1:175397/1‑113 (MQ=255)                                                                                                                   ttttACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCa                                                                  <  2:175397/113‑1 (MQ=255)                                                                                                                       acttacCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAAGTCATATAGCCAAGTAAGCTAGTcc                          <  1:591548/149‑1 (MQ=255)                                                                                                                         ttacCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCg                        >  1:242238/1‑149 (MQ=255)                                                                                                                           aacTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGaa                      <  1:415624/147‑1 (MQ=255)                                                                                                                             cTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACt                    >  1:485872/1‑149 (MQ=255)                                                                                                                              tttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTg                   <  1:329901/149‑1 (MQ=255)                                                                                                                               ttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTgg                  <  1:153898/149‑1 (MQ=255)                                                                                                                                 gTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTa                <  1:652774/149‑1 (MQ=255)                                                                                                                                 gTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCAGAACTGGTa                >  1:441945/1‑149 (MQ=255)                                                                                                                                  tATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAg               >  1:572191/1‑149 (MQ=255)                                                                                                                                  tATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAg               <  1:481118/149‑1 (MQ=255)                                                                                                                                      aGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTAc           <  2:485872/149‑1 (MQ=255)                                                                                                                                       gTAAATTTTTTTGAACAAATAAATAAAGCAAAAGTAGTTAGAAGGATTGGCTGCATGTATGCTGAGAAATTGCTTGATGTGTCTTCAACATCAGCATCGCTTAGCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACt          <  2:469548/149‑1 (MQ=255)                                                                                                                                               ttttGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCTCa  >  2:443644/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                  CTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCTCA  >  NC_000913_3_pae_tpiA/2106596‑2106886

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: ‑