Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,633,239	(T)8→7	intergenic (‑159/‑232)	uspB ← / → uspA	universal stress protein UspB/universal stress protein UspA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,633,232	0	T	.	100.0%	236.8 / NA	53	intergenic (‑152/‑239)	uspB/uspA	universal stress protein UspB/universal stress protein UspA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (29/24);  total (29/24)

CACCCCGGGGCTACCGCTCCCGATACGCTGCCAATCAGTTAACACCAGGTCCTGGAGAAACCGCTTTTGTGGTGACCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTGTTTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTATAAGGTAAGGATGGTCTTAACACTGAATCTTTACG  >  NZ_CP009273/3633113‑3633366                                                                                                                        |                                                                                                                                       cACCCCGGGGCTACCGCTCCCGATACGCTGCCAATCAGTTAACACCAGGTCCTGGAGAAACCGCTTTTGTGGTGACCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAAc                                                                                                                    <  1:536968/139‑1 (MQ=255)      cGGGGCTACCGCTCCCGATACGCTGCCAATCAGTTAACACCAGGTCCTGGAGAAACCGCTTTTGTGGTGACCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTa                                                                                                               <  1:9259/139‑1 (MQ=255)                              gCCAATCAGTTAACACCAGGTCCTGGAGAAACCGCTTTTGTGGTGACCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAAttt                                                                                       >  2:393236/1‑139 (MQ=255)                                  aTCAGTTAACACCAGGTCCTGGAGAAACCGCTTTTGTGGTGACCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGttt                                                                                   <  2:490186/139‑1 (MQ=255)                                                ggTCCTGGAGAAACCGCTTTTGTGGTGACCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAg                                                                     >  1:519880/1‑139 (MQ=255)                                                 gTCCTGGAGAAACCGCTTTTGTGGTGACCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAg                                                                     >  1:499240/1‑138 (MQ=255)                                                       gagaAACCGCTTTTGTGGTGACCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAgg                                                                <  1:134130/137‑1 (MQ=255)                                                            aCCGCTTTTGTGGTGACCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGAtt                                                          >  2:118810/1‑138 (MQ=255)                                                            aCCGCTTTTGTGGTGACCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGAtt                                                          >  2:133800/1‑138 (MQ=255)                                                            aCCGCTTTTGTGGTGACCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGAtt                                                          >  1:284349/1‑138 (MQ=255)                                                            aCCGCTTTTGTGGTGACCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGAtt                                                          >  2:219555/1‑138 (MQ=255)                                                            aCCGCTTTTGTGGTGACCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGAtt                                                          >  2:394109/1‑138 (MQ=255)                                                                           aCCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAAc                                                                                                                    <  1:359466/65‑1 (MQ=255)                                                                           aCCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAAc                                                                                                                    >  2:359466/1‑65 (MQ=255)                                                                           aCCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCggg                                           <  1:393236/138‑1 (MQ=255)                                                                           aCCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCggg                                           <  2:284349/138‑1 (MQ=255)                                                                           aCCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGt                                          >  1:451969/1‑139 (MQ=255)                                                                           aCCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGt                                          <  1:125025/139‑1 (MQ=255)                                                                           aCCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGt                                          <  1:394109/139‑1 (MQ=255)                                                                                cATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCta                                     <  2:499240/139‑1 (MQ=255)                                                                                cATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCta                                     >  1:58926/1‑139 (MQ=255)                                                                                          gCTCTATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTAtaaggtaag                            >  1:445429/1‑138 (MQ=255)                                                                                           ctctATAGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTATAAGGTAAGGa                          >  1:169894/1‑139 (MQ=255)                                                                                              tataGATAGTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTATAAGGTAAGGAt                         <  1:453756/137‑1 (MQ=255)                                                                                                     agTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTaa                                                                             <  1:478522/78‑1 (MQ=255)                                                                                                     agTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTaa                                                                             >  2:478522/1‑78 (MQ=255)                                                                                                     agTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGt                                          <  1:399773/113‑1 (MQ=255)                                                                                                     agTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGt                                          >  2:109929/1‑113 (MQ=255)                                                                                                     agTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGt                                          >  2:399773/1‑113 (MQ=255)                                                                                                     agTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGt                                          <  1:109929/113‑1 (MQ=255)                                                                                                     agTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTATAAGGTAAGGATGGTCTTaa                 >  1:493237/1‑138 (MQ=255)                                                                                                     agTGTAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTATAAGGTAAGGATGGTCTTaa                 >  2:507777/1‑138 (MQ=255)                                                                                                        gtAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGt                                          <  1:217080/110‑1 (MQ=255)                                                                                                        gtAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGt                                          >  2:217080/1‑110 (MQ=255)                                                                                                        gtAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTATAAGGTAAGGATGGTCTTAaca               <  1:364416/137‑1 (MQ=255)                                                                                                        gtAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTATAAGGTAAGGATGGTCTTAaca               >  2:364416/1‑137 (MQ=255)                                                                                                        gtAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTATAAGGTAAGGATGGTCTTAACACt             >  2:404128/1‑139 (MQ=255)                                                                                                        gtAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTATAAGGTAAGGATGGTCTTAACACt             >  2:93723/1‑139 (MQ=255)                                                                                                        gtAGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTATAAGGTAAGGATGGTCTTAACACt             >  2:236811/1‑139 (MQ=255)                                                                                                          aGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCtat                                    <  2:143102/114‑1 (MQ=255)                                                                                                          aGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCtat                                    >  1:143102/1‑114 (MQ=255)                                                                                                          aGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTATAAGGTAAGGAt                         >  2:416660/1‑125 (MQ=255)                                                                                                          aGGAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCAGCCGGGTCGCTATAAGGTAAGGAt                         <  1:416660/125‑1 (MQ=255)                                                                                                           ggAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTATAAGGTAAGGATGGTCTTAACACTGa           <  1:118810/138‑1 (MQ=255)                                                                                                           ggAGATCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTATAAGGTAAGGATGGTCTTAACACTGa           <  2:519880/138‑1 (MQ=255)                                                                                                            gagaTCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTATAAGGTAAGGATGGTCTTAACACTGAAt         >  1:350598/1‑139 (MQ=255)                                                                                                               aTCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTATAAGGTAAGGATGGTCtt                   >  1:543092/1‑126 (MQ=255)                                                                                                               aTCAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTATAAGGTAAGGATGGTCtt                   <  2:543092/126‑1 (MQ=255)                                                                                                                 cAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTc                                                                                                    <  2:35639/43‑1 (MQ=255)                                                                                                                 cAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTc                                                                                                    >  1:35639/1‑43 (MQ=255)                                                                                                                 cAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGt                                          >  2:106182/1‑101 (MQ=255)                                                                                                                 cAGGTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGt                                          <  1:106182/101‑1 (MQ=255)                                                                                                                   ggTTG‑TTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTATAAGGTAAGGATGGTCTTAACACTGAATCTTTACg  <  1:236811/139‑1 (MQ=255)                                                                                                                        |                                                                                                                                       CACCCCGGGGCTACCGCTCCCGATACGCTGCCAATCAGTTAACACCAGGTCCTGGAGAAACCGCTTTTGTGGTGACCAACATACGAGCGGCTCTATAGATAGTGTAGGAGATCAGGTTGTTTTTTTTCCAGAAGGTTAACCACTATCAATATATTCATGTCGAAAATTTGTTTATCTAACGAGTAAGCAAGGCGGATTGACGGATCATCCGGGTCGCTATAAGGTAAGGATGGTCTTAACACTGAATCTTTACG  >  NZ_CP009273/3633113‑3633366

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑