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	96.0%	151.0 / NA	51	S162S (TCT→TCA)	wbbH	O‑antigen polymerase
Reads supporting (aligned to +/- strand):  ref base A (2/0);  new base T (23/25);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 4.90e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAC  >  NC_000913_3_pae_tpiA/2106597‑2106882                                                                                                                                                 |                                                                                                                                              tctATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGAcc                                                                                                                                           >  1:629153/1‑149 (MQ=255)    aTTAACACCTACGATGAATGCATAAGAGATGATAACTCTAAAGCCCCTTTGCTTACTAGTATACAGAATACTCGTCACGTTCATTATTACAGAAATAAGTAAAGGTAATTCTTTACTAACCTGGTTAGTAGTAAAATTTTTTGATCaaa                                                                                                                                        >  2:151898/1‑149 (MQ=255)          acCTACGATGAATGCATAAGAGATGATAACCATAAAGAACATTTGCTTACCAGTATTCCGTATAAGTACAAATATGAATACAATAAAAACAAATAAAGTAAATGTTTTACTTACATTTGTATTAGTAAATTTTTTTAATCAaataaata                                                                                                                                  >  2:299200/1‑149 (MQ=255)             tACGATAAATATATAAGTAATTGTAACCTTAAAGCAACTGTTGTTACCATTATTCACTATAATAGCAAATATGAATAAAATTATTACAAGCAAAGTAAAATTTTTACTTACCTTTGTATTAGTTAATTTTTTTGACAGATTAAATAAAg                                                                                                                               <  2:116897/149‑1 (MQ=255)               cGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAGTTGCAAAGATGAATACAATCAAAACAAGTAAAGTCAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCa                                                                                                                             >  2:487237/1‑149 (MQ=255)                 aTGAAAGCATAAGAGATGATAACCATAAATACTATTTCATTAACAAAATAAAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTATCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCaaa                                                                                                                           <  1:974/149‑1 (MQ=255)                         aTAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAGCGGAAATGTTTTAACAACGATGGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTa                                                                                                                   >  1:284845/1‑149 (MQ=255)                         aTAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAATAAAGGTTTTCATTCCACAATTATGAGTAAATTTTTTTTACCAAATAAATAAAGCAAAAGTAGTTa                                                                                                                   <  1:151898/149‑1 (MQ=255)                             gaaaaaatAACCATAAATACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAAt                                                                                                               <  1:83674/143‑1 (MQ=255)                                     aaCCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCt                                                                                                       >  1:138341/1‑149 (MQ=255)                                        cATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCa                                                                                                    <  1:629207/149‑1 (MQ=255)                                         aTAAATACAATTTGCGTACTAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCAt                                                                                                   <  2:573226/149‑1 (MQ=255)                                          tAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAATACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAATCAAAATTAGTTAGAATGATTTGCTCCATg                                                                                                  >  2:24965/1‑149 (MQ=255)                                                 aaTTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGATTGATTGGCTGCATGTATGCTg                                                                                           >  2:289374/1‑149 (MQ=255)                                                 aaTTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTg                                                                                           >  1:76812/1‑149 (MQ=255)                                                  atgtGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTga                                                                                          <  2:122604/146‑1 (MQ=255)                                                   tttGCTTATCAGTATGCAATATAATTACAAAGATGAATAAAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTgag                                                                                         <  2:600272/149‑1 (MQ=255)                                                    ttGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTgg                                                                                                         >  2:505907/1‑132 (MQ=255)                                                    ttGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTgg                                                                                                         <  1:505907/132‑1 (MQ=255)                                                      gCTGACCAGTATTCACTTTAATTGCAAAGATGAATACAATAAATACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGaaa                                                                                      <  2:55733/149‑1 (MQ=255)                                                        ttACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAACGTAAATGTTTTACTTACTTTTCTATTAGTATATTATTTAGATCAAAAAAATAAAGCAAAAGAAGTAAAAATGAATGGCTACATGTATGCTGAGAAAtt                                                                                    >  1:128213/1‑149 (MQ=255)                                                        ttACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTCCACCAAAAATGGAAATCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAAtt                                                                                    >  2:458914/1‑149 (MQ=255)                                                          aCCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTc                                                                                  >  1:35417/1‑149 (MQ=255)                                                          aCCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATAATTGGCTGCATGTATGCTGAGAAATTTc                                                                                  >  2:616611/1‑149 (MQ=255)                                                            cAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATTAAACAAAAGTAGTTAGAATGATTGGCTGCATATATGCTGTGAACTTTCtt                                                                                >  2:403883/1‑149 (MQ=255)                                                               tATGCATTATAATTGCAAAGTTGAATACAATAAACACAAGTAAAGTAAATGTTTTTCTTACCTTTGTATTAGTAAATTTATATGACCAAATAAATAAAGCAAAAGAAGTTAGAATTATTGGCTGCATGTATCCCGAGAAATTCCTTGAt                                                                             <  2:528407/149‑1 (MQ=255)                                                                    aGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATCAATAAATCAAAAGTAGTTAGAATGATTGTCTGCATTTATTGTGATAAATTTCTTGAtgtttt                                                                        >  2:211101/1‑146 (MQ=255)                                                                         aaTTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCaa                                                                   <  1:371876/149‑1 (MQ=255)                                                                         aaTTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCCTCaa                                                                   <  1:48373/149‑1 (MQ=255)                                                                          aatGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAAc                                                                  <  1:127469/147‑1 (MQ=255)                                                                            tGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACAt                                                                >  1:490862/1‑149 (MQ=255)                                                                            tGCAAAGATGAATAAAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCAGGTATGCTGAGAAATTTCTTGATGTGTCTTCAACAt                                                                <  2:461549/149‑1 (MQ=255)                                                                                    tGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCAtct                                                        <  2:412505/149‑1 (MQ=255)                                                                                                    aagtaaagtaAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAACGTAGATAGAATGATTGGCTGCATGTATGAAGAGAAATAGCGTTATGTGTCTTCAATATTAGCATCTCTTATCAAATTTatct                                        >  2:458699/1‑147 (MQ=255)                                                                                                    aagtaaagtaAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCatat                                        >  1:509775/1‑149 (MQ=255)                                                                                                     agtaaagtaaATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCAtata                                       <  2:284845/149‑1 (MQ=255)                                                                                                       taaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGc                                     >  1:236094/1‑149 (MQ=255)                                                                                                            taaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaagt                                >  1:596769/1‑149 (MQ=255)                                                                                                                tGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGAACTAATAATTAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGc                            <  1:339434/149‑1 (MQ=255)                                                                                                                        ttacCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCg                    >  1:412905/1‑149 (MQ=255)                                                                                                                          acCTTTGTATTATTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGaa                  <  1:225135/149‑1 (MQ=255)                                                                                                                            cTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACt                >  1:281017/1‑149 (MQ=255)                                                                                                                             tttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaag                                 >  1:283721/1‑131 (MQ=255)                                                                                                                             tttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaag                                 <  2:283721/131‑1 (MQ=255)                                                                                                                             tttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCTAACTg               >  2:228185/1‑149 (MQ=255)                                                                                                                             tttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTg               <  2:412026/149‑1 (MQ=255)                                                                                                                               tGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGt             <  1:487237/149‑1 (MQ=255)                                                                                                                                 tATTAGTAAATTTTTTTTACCAAAAAAACAAACAAAAAGAAGGTATAATGATTGGCTGCACGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAACTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAg           <  1:339431/149‑1 (MQ=255)                                                                                                                                        aaaTTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCCTATCACTTAGTAAGCTAGTCCCGAACTGGTAGTTACTTa    <  2:462149/149‑1 (MQ=255)                                                                                                                                          aTTTTTTTTACCAAATAAATAAAGAAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATATCTTGATGTGTCTTCAAAATCAGCATCTCTTATTTAATTAATATAGCTAAGTAAGCTAGTCCCAAACTGGTTGTTACTTAAc  >  2:394784/1‑149 (MQ=255)                                                                                                                                          aTTGTTTTGACCAAATAAATAAAGCAAAAGTAGTTTGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCATCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAc  <  1:158105/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                              TCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAC  >  NC_000913_3_pae_tpiA/2106597‑2106882

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: ‑