Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,618,162	G→C	15.3%	R181G (CGT→GGT)	wzy ←	O‑antigen polymerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,618,162	0	G	C	15.3%	58.3 / 3.6	26	R181G (CGT→GGT)	wzy	O‑antigen polymerase
Reads supporting (aligned to +/- strand):  ref base G (9/12);  new base C (2/2);  total (12/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01

ACCCGGCTGTGGCGGTCACGGAACCACAACGGCGCCATCACCACGGTAATCACCAGTGCCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCAATGACATAAGCCCCCAGGATGGGGTGGGATATCTCGCCGATACCCGCCAGCCTGAACAGCAAAGGCGCACGCTGCACCCCATAGAACTTGATGATGGAG  >  NC_002947/5618020‑5618304                                                                                                                                               |                                                                                                                                               acCCGGCTGTGGCGGTCACGGAACCACAACGGCGCCATCACCACGGTAATCACCAGTGCCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACATCGCCGa                                                                                                                                         >  1:361089/1‑150 (MQ=255)   ccGGCTGTGGCGGTCACGGAACCACAACGGCGCCATCACCACGGTAATCACCAGTGCCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAgg                                                                                                                                       >  1:86991/1‑150 (MQ=255)    cGGCTGTGGCGGTCACGGAACCACAACGGCGCCATCACCACGGTAATCACCAGTGCCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGt                                                                                                                                      <  1:731577/150‑1 (MQ=255)         gtgGCGGTCACGGAACCACAACGGCGCCATCACCACGGTAATCACCAGTGCCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACCTCGGCGACGTGGCtt                                                                                                                                 <  2:686807/150‑2 (MQ=255)               gTCACGGAACCACAACGGCGCCATCACCACGGTAATCACCAGTGCCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTagag                                                                                                                           >  2:490952/1‑150 (MQ=255)                   cGGAACCACAACGGCGCCATCACCACGGTAATCACCAGTGCCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTAGAGCATc                                                                                                                       <  1:370013/150‑1 (MQ=255)                       aCCACAACGGCGCCATCACCACGGTAATCACCAGTGCCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTa                                                                                                                              >  1:41053/1‑139 (MQ=255)                       aCCACAACGGCGCCATCACCACGGTAATCACCAGTGCCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTa                                                                                                                              <  2:41053/139‑1 (MQ=255)                                     aTCACCACGGTAATCACCAGTGCCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTAGTAGAGAATCCGGAGTAGGGCTGCACCa                                                                                                     >  2:820323/1‑150 (MQ=255)                                      tCACCACGGTAATCACCAGTGCCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCaa                                                                                                    >  1:169250/1‑150 (MQ=255)                                       caccacGGTAATCACCAGTGCCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCAAt                                                                                                   <  1:295490/150‑1 (MQ=255)                                        cccacGGTAATCACCAGTACCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCAATg                                                                                                  <  2:5526/149‑1 (MQ=255)                                           acGGTAATCACCAGTGCCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTATAGCATCAAGAGCAAGGCCGAACCAATGa                                                                                                 >  1:599485/1‑148 (MQ=255)                                           acGGTAATCACCAGTGCCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTATAGCATCAAGAGCAAGGCCGAACCAATGa                                                                                                 <  2:599485/148‑1 (MQ=255)                                                    aCCAGTGCCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCAATGACATAAGccccc                                                                                      >  1:443211/1‑150 (MQ=255)                                                            cAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCAATGACATAAGCCCCCAGGATggg                                                                              <  1:490952/150‑1 (MQ=255)                                                                  cGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCAATGACATAAGCCCCCAGGATGGGGTGGGa                                                                        <  1:81784/150‑1 (MQ=255)                                                                                             gAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCAATGACATAAGCCCCCAGGATGGGGTGGGATATCTCGCCGATACCCGCCAGCCTGaa                                             <  2:443211/150‑1 (MQ=255)                                                                                                    cccAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCAATGACATAAGCCCCCAGGATGGGGTGGGATATCTCGCCGATACCCGCCAGCCTGAACAGCaaa                                      <  1:820323/150‑1 (MQ=255)                                                                                                       agccAACCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCAATGACATAAGCCCCCAGGATGGGGTGGGATATCTCGCCGATACCCGCCAGCCTGAACAGCAAAGgc                                   <  1:129594/147‑1 (MQ=255)                                                                                                                 gTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCAATGACATAAGCCCCCAGGATGGGGTGGGATATCTCGCCGATACCCGCCAGCCTGAACAGCAAAGGCGCACGCTGCa                         >  1:439604/1‑150 (MQ=255)                                                                                                                  tGCCGCCAGCCACAACAACTGGAAGCCACGTCGCCGAGGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCAATGACATAAGCCCCCAGGATGGGGTGGGATATCTCGCCGATACCCGCCAGCCTGAACAGCAAAGGCGCACGCTGCAc                        <  2:439604/150‑1 (MQ=255)                                                                                                                            cacaACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCAATGACATAAGCCCCCAGGATGGGGTGGGATATCTCGCCGATACCCGCCAGCCTGAACAGCAAAGGCGCACGCTGCACCCCATAGAAc              >  1:400514/1‑150 (MQ=255)                                                                                                                                        gaGCCACCTCGGCGACGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCAATGACATAAGCCCCCAGGATGGGGTGGGATATCTCGCCGATACCCGCCAGCCTGAACAGCAAAGGCGCACGCTGCACCCCATAGAACTtgatga       <  1:811458/144‑1 (MQ=255)                                                                                                                                        gaGCCACCTCGGCGACGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCAATGACATAAGCCCCCAGGATGGGGTGGGATATCTCGCCGATACCCGCCAGCCTGAACAGCAAAGGCGCACGCTGCACCCCATAGAACTtgatga       >  2:811458/2‑145 (MQ=255)                                                                                                                                        gaGCCACCTCGGCGACGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCAATGACATAAGCCCCCAGGATGGGGTGGGATATCTCGCCGATACCCGCCAGCCTGAACAGCAAAGGCGCACGCTGCACCCCATAGAACTTGATGATGgag  >  1:545703/2‑150 (MQ=255)                                                                                                                                               |                                                                                                                                               ACCCGGCTGTGGCGGTCACGGAACCACAACGGCGCCATCACCACGGTAATCACCAGTGCCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCAATGACATAAGCCCCCAGGATGGGGTGGGATATCTCGCCGATACCCGCCAGCCTGAACAGCAAAGGCGCACGCTGCACCCCATAGAACTTGATGATGGAG  >  NC_002947/5618020‑5618304

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑