Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	351,491	T→G	S287A (TCG→GCG)	codB →	cytosine permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	351,491	0	T	G	100.0%	173.0 / NA	47	S287A (TCG→GCG)	codB	cytosine permease
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (23/24);  total (23/24)

AGCGGGCGCTGCGGCACTGGGCATGGCGGATATCTCTGATGTGATGATTGCTCAGGGCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGTCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGTACGGTCTGCGCATTATGGCTGTATAACAATTTTGTCGGCTGGTTGACCTTCCTTTCGGCAGC  >  NZ_CP009273/351364‑351624                                                                                                                                |                                                                                                                                      aGCGGGCGCTGCGGCACTGGGCATGGCGGATATCTCTGATGTGATGATTGCTCAGGGCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGt                                                                                                                            >  1:401795/1‑139 (MQ=255)         cTGCGGCACTGGGCATGGCGGATATCTCTGATGTGATGATTGCTCAGGGTCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCaa                                                                                                                    <  1:231056/139‑1 (MQ=255)         cTGCGGCACTGGGCATGGCGGATATCTCTGATGTGATGATTGCTCAGGGCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCaa                                                                                                                    <  2:33219/139‑1 (MQ=255)                    ggCATGGCGGATATCTCTGATGTGATGATTGCTCAGGGCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGa                                                                                                         >  1:157980/1‑139 (MQ=255)                         ggCGGATATCTCTGATGTGATGATTGCTCAGGGCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGt                                                                                                                                       >  1:101263/1‑104 (MQ=255)                         ggCGGATATCTCTGATGTGATGATTGCTCAGGGCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGt                                                                                                                                       <  2:101263/104‑1 (MQ=255)                         ggCGGATATCTCTGATGTGATGATTGCTCAGGGCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCg                                                                                                    >  2:59476/1‑139 (MQ=255)                              atatCTCTGATGTGATGATTGCTCAGGGCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCaa                                                                                               <  2:159260/139‑1 (MQ=255)                              atatCTCTGATGTGATGATTGCTCAGGGCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCa                                                                                                >  2:526866/1‑138 (MQ=255)                              atatCTCTGATGTGATGATTGCTCAGGGCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGGTTCGCCAACATTACCGGGATGTCGAGCa                                                                                                >  2:353908/1‑138 (MQ=255)                                    ctGATGTGATGATTGCTCAGGGCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCaa                                                                                                                    <  2:573641/112‑1 (MQ=255)                                    ctGATGTGATGATTGCTCAGGGCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCaa                                                                                                                    >  1:573641/1‑112 (MQ=255)                                     tgatgtgatgATTGTTCAGGGCCTGCTGCTGTCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTTGCCAACCTTACCCGGATGTCGAGCAAAAcccct                                                                                        >  2:228642/1‑137 (MQ=255)                                            atgatTGCTCAGGGCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGGTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTaa                                                                                 >  2:199822/1‑139 (MQ=255)                                               atTGCTCAGGGCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCa                                                                              <  1:748365/139‑1 (MQ=255)                                                  gCTCAGGGCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAAc                                                                            <  1:300444/138‑1 (MQ=255)                                                   cTCAGGGCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACgg                                                                          >  1:118797/1‑139 (MQ=255)                                                      aGGGCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGt                                                                         <  2:526573/137‑1 (MQ=255)                                                        ggCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGtatta                                                                     <  1:228642/139‑1 (MQ=255)                                                        ggCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGtatta                                                                     <  1:72983/139‑1 (MQ=255)                                                             gctgctgcCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCaa                                                                                                                    <  2:51215/87‑1 (MQ=255)                                                             gctgctgcCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCaa                                                                                                                    >  1:51215/1‑87 (MQ=255)                                                             gctgctgcCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGGTGTCGAGCAAAAACCTTTCGGTAATCAACGGTATTATCgg                                                                 >  2:193590/1‑138 (MQ=255)                                                             gctgctgcCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGt                                                                                                      >  2:246890/1‑101 (MQ=255)                                                             gctgctgcCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGt                                                                                                      <  1:246890/101‑1 (MQ=255)                                                             gctgctgcCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCgg                                                                 >  1:615744/1‑138 (MQ=255)                                                              ctgctgcCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGt                                                                <  1:59476/138‑1 (MQ=255)                                                              ctgctgcCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGt                                                                <  2:157980/138‑1 (MQ=255)                                                              ctgctgcCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGt                                                                <  1:526866/138‑1 (MQ=255)                                                                   gcctgcGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGt                                                                         >  2:182589/1‑124 (MQ=255)                                                                   gcctgcGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGt                                                                         <  1:182589/124‑1 (MQ=255)                                                                     ctgcGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGTACGGTCTg                                                        <  1:605712/139‑1 (MQ=255)                                                                     ctgcGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGTACGGTCTg                                                        <  2:470072/139‑1 (MQ=255)                                                                     ctgcGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGTACGGTCTg                                                        <  2:401795/139‑1 (MQ=255)                                                                                gtgCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGTACGGTCTGCGCATTATgg                                              <  2:624238/138‑1 (MQ=255)                                                                                   cTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGTACGGTCTGCGCATTATGGCTg                                           >  1:40882/1‑138 (MQ=255)                                                                                        gCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGTACGGTCTg                                                        <  2:460068/120‑1 (MQ=255)                                                                                        gCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGTACGGTCTg                                                        >  1:460068/1‑120 (MQ=255)                                                                                        gCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGTACGGTCTGCGCATTATGGCTGTATaa                                      >  1:23963/1‑138 (MQ=255)                                                                                                  tGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAg                                                                                                  >  1:681400/1‑68 (MQ=255)                                                                                                  tGGACCACCAACGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAg                                                                                                  <  2:681400/68‑1 (MQ=255)                                                                                                      ccaccaACGATAACGCACTCTATGCGGCGGGTTTAGGGTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGTACGGTCTGCGCATTATGGCTGTATAAAAATTTTGTCGGCTg                       >  2:499979/1‑139 (MQ=255)                                                                                                         ccaACGATAACGCACTCTATGCGGCGGGTTTAGGGTTCTCCCACCTTACCCGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCCGTACCGTCTGCGCATTATGGCTGGATAACAATTTTTTCGGCCgggt                    >  1:122172/1‑137 (MQ=255)                                                                                                             cGATAACGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGTACGGTCTGCGCATTATGGCTGTATAACAATTTTGTCGGCTGGTTGAcc                <  2:122172/139‑1 (MQ=255)                                                                                                                 aaCGCACTCTATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGTACGGTCTGCGCATTATGGCTGTATAACAATTTTGTCGGCTGGTTGAacttcc            >  2:674560/1‑139 (MQ=255)                                                                                                                   cGCACTCTATGCGGCGGGTTTTAGTTTCGCCAACATTACCGGGATGTCGAGCCAAAACCTTTCGGTAATCAACGGGATTATCGGTACGGTCTGCGCATTATGGCTGTATTACAATTTTGTCGGCTTGTTGTccttcctt          >  2:151804/1‑139 (MQ=255)                                                                                                                          tATGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGTACGGTCTGCGCATTATGGCTGTATAACAATTTTGTCGGCTGGTTGACCTTCCTTTCGGCAg   >  1:186785/1‑139 (MQ=255)                                                                                                                            tGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGTACGGTCTGCGCATTATGGCTGTATAACAATTTTGTCGGCTGGTTGACCTTCCTTTCGGCa    <  2:62490/136‑1 (MQ=255)                                                                                                                            tGCGGCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGTACGGTCTGCGCATTATGGCTGTATAACAATTTTGTCGGCTGGTTGACCTTCCTTTCGGCAGc  <  1:353908/138‑1 (MQ=255)                                                                                                                                |                                                                                                                                      AGCGGGCGCTGCGGCACTGGGCATGGCGGATATCTCTGATGTGATGATTGCTCAGGGCCTGCTGCTGCCTGCGATTGTGGTGCTGGGGCTGAATATCTGGACCACCAACGATAACGCACTCTATGCGTCGGGTTTAGGTTTCGCCAACATTACCGGGATGTCGAGCAAAACCCTTTCGGTAATCAACGGTATTATCGGTACGGTCTGCGCATTATGGCTGTATAACAATTTTGTCGGCTGGTTGACCTTCCTTTCGGCAGC  >  NZ_CP009273/351364‑351624

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑