BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,618,170	G→C	16.7%	P178R (CCT→CGT)	wzy ←	O‑antigen polymerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,618,170	0	G	C	16.7%	51.3 / 6.4	24	P178R (CCT→CGT)	wzy	O‑antigen polymerase
Reads supporting (aligned to +/- strand): ref base G (8/12); new base C (2/2); total (10/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.49e-01

CCGGCTGTGGCGGTCACGGAACCACAACGGCGCCATCACCACGGTAATCACCAGTGCCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCAATGACATAAGCCCCCAGGATGGGGTGGGATATCTCGCCGATACCCGCCAGCCTGAACAGCAAAGGCGCACGCTGCACCCCATAGAACTTGATGATGGAG  >  NC_002947/5618022‑5618304

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)

CCGGCTGTGGCGGTCACGGAACCACAACGGCGCCATCACCACGGTAATCACCAGTGCCAGAACCGCACCACGGCTCTGGCTGAGCATGGCGAAGGCCCCCAGGCAAGCCAGTGCCGCCAGCCACAACAACTGCAAGCCACGTCGCCGAGGTGGCTCGTAGAGCATCAAGAGCAAGGCCGAACCAATGACATAAGCCCCCAGGATGGGGTGGGATATCTCGCCGATACCCGCCAGCCTGAACAGCAAAGGCGCACGCTGCACCCCATAGAACTTGATGATGGAG  >  NC_002947/5618022‑5618304

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`