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%	170.2 / NA	56	S162S (TCT→TCA)	wbbH	O‑antigen polymerase
Reads supporting (aligned to +/- strand):  ref base A (0/1);  major base T (31/23);  minor base C (0/1);  total (31/25)
Fisher's exact test for biased strand distribution p-value = 4.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACC  >  NC_000913_3_pae_tpiA/2106596‑2106883                                                                                                                                                  |                                                                                                                                               ctctATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGAc                                                                                                                                             >  1:888278/1‑149 (MQ=255)    tATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTTACCaa                                                                                                                                          >  2:375373/1‑149 (MQ=255)    tATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTA‑TAGTAAATTTTTTTGACCaaa                                                                                                                                         >  2:570722/1‑149 (MQ=255)      ttAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaat                                                                                                                                        >  2:746234/1‑149 (MQ=255)             cTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAAtaaataaa                                                                                                                                 <  2:523206/149‑1 (MQ=255)             cTACGATAAATGCATAAGAGATGATAACAATAAAGACAATTTGCAGAACAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAAtaaataaa                                                                                                                                 <  2:106628/149‑1 (MQ=255)              tACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTATTTTTTTTTGTTCAAATAAATAAAg                                                                                                                                >  2:785700/1‑149 (MQ=255)                cGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCa                                                                                                                              <  2:672511/149‑1 (MQ=255)                 gATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGTTCATATAAATAAAGCaa                                                                                                                             >  2:906468/1‑149 (MQ=255)                         gaTACGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAATTGTTTTCCTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGtt                                                                                                                     >  2:792418/2‑149 (MQ=255)                            aaGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGa                                                                                                                  >  1:636429/1‑149 (MQ=255)                                gatgatAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGa                                                                                                              >  1:1011670/1‑149 (MQ=255)                                  tgatAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGAtt                                                                                                            <  1:728748/149‑1 (MQ=255)                                    atAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTgg                                                                                                          <  2:888278/149‑1 (MQ=255)                                      aaCCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCt                                                                                                        >  1:607868/1‑149 (MQ=255)                                      aaCCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACATTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCt                                                                                                        >  1:206019/1‑149 (MQ=255)                                         cATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTAACCAAATAAATAAAGCAAACGTACTTACACTGATTGAATGCa                                                                                                     >  2:777437/1‑149 (MQ=255)                                           tAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATg                                                                                                   >  2:691701/1‑149 (MQ=255)                                             aaGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTa                                                                                                 >  1:8237/1‑149 (MQ=255)                                              aGACAATTTGCTTACCAGTGTTCAGTATAATTGCAAAGATGAATACAATAAAACCAAGTACAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGCCCAAATAAATAAAGCAAAAGTAGTTAGAATCATTCGCTGCATGtct                                                                                                >  2:884335/1‑147 (MQ=255)                                               gaaaaTATGCTTACCAATATTCAGTATAATTTCAAATATGAATAAAATAAAAACAAGTAAAGTAAATGTTTTACGAATCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATg                                                                                               <  1:824444/146‑1 (MQ=255)                                                   aTTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTga                                                                                           >  1:402674/1‑149 (MQ=255)                                                             cAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt                                                                                 <  2:866605/149‑1 (MQ=255)                                                             cAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGACTGCATGTATGCTGAGAAATTTCtt                                                                                 >  1:181715/1‑149 (MQ=255)                                                                tATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt                                                                              <  2:402674/149‑1 (MQ=255)                                                                tATTCAGTATAATTGCAAAAATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAAtttataaaa                                                                              >  2:255658/1‑143 (MQ=255)                                                                    cAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATgtgt                                                                          <  2:455962/149‑1 (MQ=255)                                                                       tataATTGCAAAGATGAATACAATAGAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTGAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCtt                                                                       <  1:943364/149‑1 (MQ=255)                                                                       tataATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTAACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCtt                                                                       >  1:52905/1‑149 (MQ=255)                                                                        ataATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACGTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTc                                                                      >  1:933730/1‑149 (MQ=255)                                                                          aaTTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTTTTTTTTTATTTAAAGCAAAAGTAGTTAGAATGAGTGGCTGCATGTATGTTGAGAAATTTCTTGATGTTTCTTCaa                                                                    >  2:657336/1‑149 (MQ=255)                                                                              gCAAAGATAAAGACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAACAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGATAAATTTCTTGATGTGTCTTCAACATc                                                                <  2:699219/149‑1 (MQ=255)                                                                               cAAAGATTAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACTTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCa                                                               <  1:146381/149‑1 (MQ=255)                                                                               cAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCa                                                               <  1:893124/149‑1 (MQ=255)                                                                                    aTGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACAAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCAtc                                                          <  1:828129/149‑1 (MQ=255)                                                                                    aTGAATACAATAAAAACAAGTAAAGTAAATCTTTTACTTACCGTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTCTATGTATCCTGAGAAATTTCTTGATGTTCCTTCAACATCAGCAtc                                                          >  2:451851/1‑149 (MQ=255)                                                                                      gAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCAtctc                                                        >  1:543978/1‑149 (MQ=255)                                                                                      gAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATAAGCAtctc                                                        >  1:396533/1‑149 (MQ=255)                                                                                       aaTACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCAtctc                                                        <  2:1001827/148‑1 (MQ=255)                                                                                       aaTACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCAtctc                                                        >  1:1001827/1‑148 (MQ=255)                                                                                         tACAATAAAAACAAGTAAAGTAAATATTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTa                                                     <  2:37641/149‑1 (MQ=255)                                                                                             aTAAAAACAAGTAAATAAAATGTTTAACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTGATAATGATTGGCTGCATGTATGCGGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCaa                                                 <  1:481038/149‑1 (MQ=255)                                                                                             aTAAAAACAAGGAAAGTAAAGTTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCaa                                                 <  1:656480/149‑1 (MQ=255)                                                                                                aaaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAAtt                                              <  1:436312/149‑1 (MQ=255)                                                                                                    cAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCata                                          >  1:108382/1‑149 (MQ=255)                                                                                                           agtaaaTGTTTTACTTACGTTTGTATTAGTAAATTTTTTCGACCTAACAAATAAAGCAAAAGTAGTTAGAATGATTGGCAGCATGTATGCTGAGAAATTTCTTGACGTGTCTTCAACATCAGCTTCTCTTATCAAATTCATATAGCtaa                                   <  1:792418/149‑1 (MQ=255)                                                                                                           agtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaa                                   >  1:735301/1‑149 (MQ=255)                                                                                                                        cttacCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTccc                      <  1:746234/149‑1 (MQ=255)                                                                                                                         ttacCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGATAGTCACg                     >  1:955649/1‑149 (MQ=255)                                                                                                                             cTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACt                 >  1:1028293/1‑149 (MQ=255)                                                                                                                              tttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTg                >  1:599651/1‑149 (MQ=255)                                                                                                                                 gTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTa             <  1:247516/149‑1 (MQ=255)                                                                                                                                   aTTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTc                                                                         <  2:373335/87‑1 (MQ=255)                                                                                                                                   aTTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTc                                                                         >  1:373335/1‑87 (MQ=255)                                                                                                                                            ttttttTGACCAAAAAAATAAAGCAAAAGTACTTAGAATAAATGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAcc  <  1:112547/149‑1 (MQ=255)                                                                                                                                            ctctttACAGCAGATAAAAAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAcc  <  2:213485/146‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                               CTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACC  >  NC_000913_3_pae_tpiA/2106596‑2106883

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: ‑