Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,527,562	A→G	L140P (CTG→CCG)	sgcA ←	putative phosphotransferase enzyme IIA component

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,527,562	0	A	G	100.0%	202.6 / NA	55	L140P (CTG→CCG)	sgcA	putative phosphotransferase enzyme IIA component
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (29/26);  total (29/26)

AATATCCAGATGCAGGCTCCCAAAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCAGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGACGCAGAGAAGCAG  >  NC_000913/4527436‑4527695                                                                                                                               |                                                                                                                                      aaTATCCAGATGCAGGCTCCCAAAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGgc                                                                                                                                     >  1:899335/1‑129 (MQ=255)   tatCCAGATGCAGGCTCCCAAAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCa                                                                                                                         <  2:732134/139‑1 (MQ=255)      ccAGATGCAGGCTCCCAAAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCg                                                                                                                      >  1:830026/1‑139 (MQ=255)        aGATGCAGGCTCCCAAAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTc                                                                                                                    <  1:273199/139‑1 (MQ=255)          aTGCAGGCTCCCAAAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGc                                                                                                                          <  1:559729/131‑1 (MQ=255)          aTGCAGGCTCCCAAAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGc                                                                                                                          >  2:559729/1‑131 (MQ=255)              aGGCTCCC‑AAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTg                                                                                                             <  2:258846/139‑1 (MQ=255)                    ccAAAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCAtt                                                                                                        >  2:1010744/1‑139 (MQ=255)                           ccAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACt                                                                                                 <  1:1010744/139‑1 (MQ=255)                              gATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGcc                                                                                              >  2:1022005/1‑139 (MQ=255)                                 tGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGtt                                                                                           <  1:20708/139‑1 (MQ=255)                                             tCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGc                                                                               >  2:793057/1‑139 (MQ=255)                                              cAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCg                                                                              <  2:830026/139‑1 (MQ=255)                                                      gACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATa                                                                      >  1:1135210/1‑139 (MQ=255)                                                                   agGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAAc                                                                                                                               >  2:720333/1‑69 (MQ=255)                                                                   agGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAAc                                                                                                                               <  1:720333/69‑1 (MQ=255)                                                                   agGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATgc                                                         >  1:1308411/1‑139 (MQ=255)                                                                   agGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATgc                                                         >  1:159168/1‑139 (MQ=255)                                                                        ttGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGa                                                    >  2:141773/1‑139 (MQ=255)                                                                         tGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGaa                                                   <  1:141773/139‑1 (MQ=255)                                                                         tGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGaa                                                   <  2:1135210/139‑1 (MQ=255)                                                                             cTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGt                                               <  2:1308411/139‑1 (MQ=255)                                                                               ggCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGt                                                                                                                     >  1:1107983/1‑67 (MQ=255)                                                                               ggCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGt                                                                                                                     <  2:1107983/67‑1 (MQ=255)                                                                               ggCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCa                                             >  1:619181/1‑139 (MQ=255)                                                                                gCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCaa                                            <  2:619181/139‑1 (MQ=255)                                                                                 cGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCaaa                                           <  2:159168/139‑1 (MQ=255)                                                                                          ggTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTg                                                             <  2:1257889/112‑1 (MQ=255)                                                                                          ggTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTg                                                             >  1:1257889/1‑112 (MQ=255)                                                                                          ggTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGa                                                    <  2:901169/121‑1 (MQ=255)                                                                                          ggTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGa                                                    >  1:901169/1‑121 (MQ=255)                                                                                          ggTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCg                                  >  1:339838/1‑139 (MQ=255)                                                                                            tGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGaa                                                   >  1:326612/1‑120 (MQ=255)                                                                                            tGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGaa                                                   <  2:326612/120‑1 (MQ=255)                                                                                                         gcgcCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGgcg                   >  2:23038/1‑139 (MQ=255)                                                                                                           gcCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCa                                                                                                          >  1:1077779/1‑50 (MQ=255)                                                                                                           gcCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCa                                                                                                          <  2:1077779/50‑1 (MQ=255)                                                                                                           gcCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGAt                                                           >  1:60236/1‑97 (MQ=255)                                                                                                           gcCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGAt                                                           <  2:60236/97‑1 (MQ=255)                                                                                                            ccTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTg                >  1:1177058/1‑139 (MQ=255)                                                                                                             cTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTTTGTGCGGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGTTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGa               >  1:879831/1‑139 (MQ=255)                                                                                                             cTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGa               >  1:492204/1‑139 (MQ=255)                                                                                                              tCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCg                                                                              <  1:756470/75‑1 (MQ=255)                                                                                                              tCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCg                                                                              >  2:756470/1‑75 (MQ=255)                                                                                                              tCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATAtgtg                                    >  2:1144963/1‑117 (MQ=255)                                                                                                              tCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATAtgtg                                    <  1:1144963/117‑1 (MQ=255)                                                                                                               ccGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGACg             >  2:1044180/1‑139 (MQ=255)                                                                                                                 gTTAACCTGATACCGGCGCAAACAGTGCATCGTCTCTGCTGGCATTTCCCACTGCCGTTAAGCATTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGACGCa           <  1:793057/139‑1 (MQ=255)                                                                                                                     aCCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGACGCAgaga       <  1:23038/139‑1 (MQ=255)                                                                                                                       cTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGACGCAGAGAag     <  2:879831/139‑1 (MQ=255)                                                                                                                         gATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGACGCAGAGAagca   <  1:1022005/139‑1 (MQ=255)                                                                                                                          aTACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCg                                  >  2:669708/1‑107 (MQ=255)                                                                                                                          aTACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCg                                  <  1:669708/107‑1 (MQ=255)                                                                                                                          aTACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGACGCAGAGAagcag  >  2:613351/1‑139 (MQ=255)                                                                                                                          aTACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGACGCAGAGAagcag  >  1:590481/1‑139 (MQ=255)                                                                                                                               |                                                                                                                                      AATATCCAGATGCAGGCTCCCAAAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCAGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGACGCAGAGAAGCAG  >  NC_000913/4527436‑4527695

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑