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	95.5%	59.3 / NA	22	S162S (TCT→TCA)	wbbH	O‑antigen polymerase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (12/9);  minor base G (0/1);  total (12/10)
Fisher's exact test for biased strand distribution p-value = 4.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCA‑TATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCTCA  >  NC_000913_3_pae_tpiA/2106609‑2106886                                                                                                                                     |                                                                                                                                                   tACGATGAATGCATAAGAGATGCTAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATAAATACAATAAAAACAAATAAAGTACATGTTTTACTTACCTTTGTATAAGTAAATTACTTTCAACAAATAAATCAAg                                                                                                                                    >  2:227568/1‑149 (MQ=255)    gATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTATTTACCTTTGTATTTGTAAATTTTTTTGATCAAATAATTATAGCac                                                                                                                                 >  2:76051/1‑148 (MQ=255)          tGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAagtag                                                                                                                           >  1:286554/1‑149 (MQ=255)              tAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAg                                                                                                                       >  2:479161/1‑149 (MQ=255)                                aaaaCAATTCGCTTACCAGTATTCAGGAGAATTGGAAAGATGAATACAAGAAAAACAAGAAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTGGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTa                                                                                                     <  2:41406/146‑1 (MQ=255)                                       tttGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTgag                                                                                              >  2:466614/1‑149 (MQ=255)                                                cAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt                                                                                     >  1:333346/1‑149 (MQ=255)                                                 aGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTg                                                                                    <  1:479161/149‑1 (MQ=255)                                                   tATTAAGTATAATTGCAAAGATGAATACAAGAAAAACAAGTATAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt                                                                                  <  2:452107/149‑1 (MQ=255)                                                     ttgaGTATAATAGCAAAGATGCATTGAATGAAAACAAGTAACGAAAATGTTTTATTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt                                                                                <  2:330023/146‑1 (MQ=255)                                                     ttCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTTCTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt                                                                                >  1:328852/1‑149 (MQ=255)                                                     ttCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGGTGAGAAATTTCTTGAtga                                                                                >  1:452107/1‑148 (MQ=255)                                                     ttCAGTATAATTGAAAAGATGAATACAAAAAAAACAAATAACGTAAATGGTTTACTTACCTTTGTATTAGTAAAGTTTTTTCACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt                                                                                <  2:206615/149‑1 (MQ=255)                                                        aGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTc                                                                             >  1:238345/1‑149 (MQ=255)                                                                            tACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCGTCTCTTa                                                         >  1:252831/1‑149 (MQ=255)                                                                                     aaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCa                                                >  2:276359/1‑149 (MQ=255)                                                                                                taaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCA‑TATAGCtaatt                                    >  2:62743/1‑147 (MQ=255)                                                                                                           cttatCTTTGTCTTCTTATATCCTTTTGAGCAAATAAATAAAGCAAAAGTAGTTAGAATTATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACCTCAGCATCTCTTATCAAATTCA‑TATAGCTAAGTAAGCTAGTccc                         <  1:240219/149‑1 (MQ=255)                                                                                                                    tgaatAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGATGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCA‑TATAGCTAAGTAAGCTAGTCCCGAACTGGTa                <  2:247912/145‑1 (MQ=255)                                                                                                                    gTATTAGTAAATTGTTTTGACCAAATAAATAAAGCAAAAGTAGGTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCA‑TATAGCTAAGTAAGCTAGTCCCGAACTGGTa                <  2:248278/149‑1 (MQ=255)                                                                                                                           tAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCACTACTG‑GAGTTAAGCTAGTCCCGAACTGGTAGTTACtt         <  1:246033/149‑1 (MQ=255)                                                                                                                              aTTTTTTTGACCAAAGAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCA‑TATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAc      <  2:328852/149‑1 (MQ=255)                                                                                                                                  ttttGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCCTGTCTATCTACGAGTTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCA‑TATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCTCa  <  1:466614/149‑1 (MQ=255)                                                                                                                                     |                                                                                                                                                   TACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCA‑TATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCTCA  >  NC_000913_3_pae_tpiA/2106609‑2106886

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: ‑