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%	178.3 / ‑3.3	55	coding (486/1167 nt)	wbbH	O‑antigen polymerase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (23/31);  minor base . (1/0);  total (24/31)
Fisher's exact test for biased strand distribution p-value = 4.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.35e-01

ACTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAC  >  NC_000913_3_pae_tpiA/2106595‑2106882                                                                                                                                                   |                                                                                                                                              aCTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGa                                                                                                                                             <  2:372533/149‑1 (MQ=255) aCTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGa                                                                                                                                             <  2:683814/149‑1 (MQ=255)      aTTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaa                                                                                                                                        <  2:762084/149‑1 (MQ=255)         aaCACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaataa                                                                                                                                     >  1:158781/1‑149 (MQ=255)               tACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTT‑GACCAAATAAATAAAGc                                                                                                                              >  1:745638/1‑149 (MQ=255)                   aTGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGGATTCAGTATAATTGCAAAGATAAATACAATAAAAAAAATTAAAGTAAATGTTTTATTTACCATTGTATTAGTAAATTTTTTTGACCAaataaatacggaaaa                                                                                                                           >  2:703635/1‑142 (MQ=255)                    tGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCaaaa                                                                                                                          <  1:216343/149‑1 (MQ=255)                    tGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATAAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCaaaa                                                                                                                          <  1:395557/149‑1 (MQ=255)                                   tgatAACAATAAAGACAATTTGATTAACAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGAtt                                                                                                           <  2:659709/149‑1 (MQ=255)                                       aaCCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAATCAAAAGTAGTTAGAATGATTGGCt                                                                                                       >  2:260619/1‑149 (MQ=255)                                         ccATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGACGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGc                                                                                                     >  1:741625/1‑149 (MQ=255)                                          cATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCa                                                                                                    >  2:589846/1‑149 (MQ=255)                                           aTAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCAt                                                                                                   <  1:630565/149‑1 (MQ=255)                                                 aCAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGc                                                                                             <  2:359418/149‑1 (MQ=255)                                                  cAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCt                                                                                            <  1:407616/149‑1 (MQ=255)                                                  cAATATGCTTACCAGTATTCAGTATAATTTCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCt                                                                                            <  1:547068/149‑1 (MQ=255)                                                   aaTTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTg                                                                                           >  1:479488/1‑149 (MQ=255)                                                   aaTTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTg                                                                                           >  1:328519/1‑149 (MQ=255)                                                          ttACCAGTGTTCAGTATAAATGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATGAGTAAATTTTTTTGAGCGAATAAATAGAGCAAAAGTAGTTAGAACGAATAGCTGCATGTATGCTGAGAAAtt                                                                                    >  2:791608/1‑149 (MQ=255)                                                             ccAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATAAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATTTATGCTGCGAAATTTCt                                                                                 >  2:407996/1‑149 (MQ=255)                                                              cAGTATTTATTATAATTGCAAAGAAGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt                                                                                <  1:309099/149‑1 (MQ=255)                                                                gTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGATGCATGTATGCTGACAAATTTCTTGa                                                                              >  2:850229/1‑149 (MQ=255)                                                                 tATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt                                                                             <  1:252115/149‑1 (MQ=255)                                                                   ttaaGTTTAATTGCAAAGATGAAGACAATAAAAACGAGTAAAGTAAATGTTTTACTTACTTTTGTTCTAGTAAAATTTTTTATCACATTATATAAAAAAAAATTAATTAGAATGATTAAGTCTATGTATACTTAGATATTTCTTggttt                                                                           >  2:761943/4‑145 (MQ=255)                                                                        tataATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAagtagt                                                                                                                     <  1:378587/102‑1 (MQ=255)                                                                        tataATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAagtagt                                                                                                                     >  2:378587/1‑102 (MQ=255)                                                                           aaTTGTAAATATTAATACAATAAAAACAAGGAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCaa                                                                   <  1:169696/149‑1 (MQ=255)                                                                           aaTTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCaa                                                                   >  1:88258/1‑149 (MQ=255)                                                                           aaTGGCAAAGATTAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCaa                                                                   <  1:169686/149‑1 (MQ=255)                                                                               gCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAACCAATCAGAGGGAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATc                                                               >  1:688790/1‑149 (MQ=255)                                                                                gaagaaTGAATGCAATCACATCAAGAACAGTAAATGTTGTAGTGAGGTTTGTATTAGTATATCTTTGTGAGCAAAAATAAAAAGCAAAACTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCa                                                              <  2:891301/144‑1 (MQ=255)                                                                                 aaaGATTAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAg                                                             <  1:188575/149‑1 (MQ=255)                                                                                           aCAATAAACATAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTAt                                                   <  1:35674/149‑1 (MQ=255)                                                                                                 aaaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAAtt                                             <  1:575000/149‑1 (MQ=255)                                                                                                  aaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTc                                            <  2:841589/149‑1 (MQ=255)                                                                                                    aCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCat                                          >  2:60637/1‑149 (MQ=255)                                                                                                      aagtaaagtaAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCatat                                        <  1:633839/149‑1 (MQ=255)                                                                                                        gtaaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt                                                                             <  2:294383/110‑1 (MQ=255)                                                                                                        gtaaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt                                                                             >  1:294383/1‑110 (MQ=255)                                                                                                         taaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCCGCATCTCTTATCAAATTCATATAGc                                     >  1:86183/1‑149 (MQ=255)                                                                                                          aaagtaaaTGTGTTACTTATCCTTGTATTAGTAAAATTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGAATGGCTGCATGTATCCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCt                                    <  2:843018/149‑1 (MQ=255)                                                                                                            agtaaaTTTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTATAATGATTGGCTGCATGTAGGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaa                                  <  2:816994/149‑1 (MQ=255)                                                                                                             gtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGCTGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtagg                                 >  1:354463/1‑147 (MQ=255)                                                                                                                  tGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGc                            <  2:158781/149‑1 (MQ=255)                                                                                                                  tGTTCTACTTACCTTTGTATTAGAAAATTTTTTTGACCAAATAAACAAAGCAAAAGTAGTTATAATGATTGGCTGCATTTATGCTGACAAACTTATTGTTGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGc                            <  1:791608/149‑1 (MQ=255)                                                                                                                    ttttACTTACCTTTGTATTAGTAAATTTTTTTGACCACTCTAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTa                          >  1:925161/1‑149 (MQ=255)                                                                                                                    ttttACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAACATCTCTTATCAAATTCATATAGCTAAGTAAGCTa                          >  2:613364/1‑149 (MQ=255)                                                                                                                              cTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACt                >  1:338021/1‑149 (MQ=255)                                                                                                                              cTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGGTAGAATGATTGACTGCATAAAAGCTAAGAAATTTCTTGATGTTTCTTCAACATCAGCATCTCTTTTCAAATTCATATAGACATGTAATCTAGTCACGAACt                >  2:738911/1‑149 (MQ=255)                                                                                                                                 tGTATTAGTAAATTTTTTTGACCAAATCAATAAATCAAACGTAGATATAATGATTGCCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGt             <  2:666472/149‑1 (MQ=255)                                                                                                                                     ttAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAATTACAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGtt         <  1:260619/149‑1 (MQ=255)                                                                                                                                      tAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTa        <  1:589846/149‑1 (MQ=255)                                                                                                                                      tAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTa        >  1:720491/1‑149 (MQ=255)                                                                                                                                           aaTTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTaa   <  2:720491/149‑1 (MQ=255)                                                                                                                                            aTTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAc  <  2:88258/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                              ACTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAC  >  NC_000913_3_pae_tpiA/2106595‑2106882

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑