Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,357,276	C→T	G448S (GGC→AGC)	cadA ←	lysine decarboxylase, acid‑inducible

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,357,276	0	C	T	100.0%	182.6 / NA	57	G448S (GGC→AGC)	cadA	lysine decarboxylase, acid‑inducible
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (31/26);  total (31/26)

CTTTGATCGGGTCAAGATACATGTGCTCGTTATCGATGTTTTTGAAGCCGTGCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCCATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTGCCTTTCATCATCGCCGCAGCGGTTTCAGTGGACGCCACGATACCGT  >  NC_000913/4357147‑4357410                                                                                                                                  |                                                                                                                                       cTTTGATCGGGTCAAGATACATGTGCTCGTTATCGATGTTTTTGAAGCCGTGCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTc                                                                                                                               >  2:512225/1‑139 (MQ=255)      aTCGGGTCAAGATACATGTGCTCGTTATCGATGTTTTTGAAGCCGTGCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTtc                                                                                                                          >  2:1165371/1‑139 (MQ=255)        cGGGTCAACATACATGTGCTCGTTATCGATGTTTTTGAAGCCGTGCCAGGTGCTGTCAGAACGCAGCGGCCAGCATGCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTtctc                                                                                                                        <  1:851465/139‑1 (MQ=255)         gggTCAAGATACATGTGCTCGTTATCGATGTTTTTGAAGCCGTGCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCa                                                                                                                       <  1:1181586/139‑1 (MQ=255)                          cTCGTTATCGATGTTTTTGAAGCCGTGCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCa                                                                                                                       >  2:14902/1‑122 (MQ=255)                          cTCGTTATCGATGTTTTTGAAGCCGTGCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCa                                                                                                                       <  1:14902/122‑1 (MQ=255)                          cTCGTTATCGATGTTTTTGAAGCCGTGCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTa                                                                                                      >  1:275326/1‑139 (MQ=255)                          cTCGTTATCGATGTTTTTGAAGCCGTGCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTa                                                                                                      >  2:520609/1‑139 (MQ=255)                           tCGTTATCGATGTTTTTGAAGCCGTGCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGAtc                                                                                                            <  2:1230353/132‑1 (MQ=255)                           tCGTTATCGATGTTTTTGAAGCCGTGCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGAtc                                                                                                            >  1:1230353/1‑132 (MQ=255)                                      gTTTTTGAAGCCGTGCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATc                                                                                          <  1:1015879/139‑1 (MQ=255)                                        ttttGAAGCCGTGCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGc                                                                                        <  1:520411/139‑1 (MQ=255)                                           tGAAGCCGTGCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACg                                                                                     <  1:171478/139‑1 (MQ=255)                                               gCCGTGCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCa                                                                                 >  1:914807/1‑139 (MQ=255)                                                   tGCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAg                                                                             <  2:782675/139‑1 (MQ=255)                                                   tGCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAg                                                                             >  2:176240/1‑139 (MQ=255)                                                    gCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGa                                                                            >  1:115929/1‑139 (MQ=255)                                                    gCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGa                                                                            >  2:996904/1‑139 (MQ=255)                                                             tGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGAt                                                                   >  2:171299/1‑139 (MQ=255)                                                              gTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATc                                                                  <  1:512225/139‑1 (MQ=255)                                                                   aaCGCAGCTGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACg                                                             <  2:148395/139‑1 (MQ=255)                                                                   aaCGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGa                                                                                                              <  1:1072108/90‑1 (MQ=255)                                                                   aaCGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGa                                                                                                              >  2:1072108/1‑90 (MQ=255)                                                                        aGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTAc                                                        >  1:1176892/1‑139 (MQ=255)                                                                         gCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGa                                                                                                                     <  1:1076908/77‑1 (MQ=255)                                                                         gCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGa                                                                                                                     >  2:1076908/1‑77 (MQ=255)                                                                              cAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTACAt                                                  <  2:914807/139‑1 (MQ=255)                                                                                                atatGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATa                                                                              >  1:1281114/1‑93 (MQ=255)                                                                                                atatGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATa                                                                              <  2:1281114/93‑1 (MQ=255)                                                                                                  atGATCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTGCCTTTCATCATCGCCGCa                              <  2:275326/139‑1 (MQ=255)                                                                                                      tCCGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTGCCTTTCATCATCGCCGCAGCgg                          >  1:1069291/1‑139 (MQ=255)                                                                                                        cGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACg                                                                                     <  1:1044168/78‑1 (MQ=255)                                                                                                        cGGCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACg                                                                                     >  2:1044168/1‑78 (MQ=255)                                                                                                         ggCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAAtt                                                                                               >  2:605522/1‑67 (MQ=255)                                                                                                         ggCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAAtt                                                                                               <  1:605522/67‑1 (MQ=255)                                                                                                          gCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGAt                                                                                                             <  2:210856/52‑1 (MQ=255)                                                                                                          gCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGAt                                                                                                             >  1:210856/1‑52 (MQ=255)                                                                                                          gCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACg                                                                                     >  1:518264/1‑76 (MQ=255)                                                                                                          gCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACg                                                                                     <  2:518264/76‑1 (MQ=255)                                                                                                          gCTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTGCCTTTCATCATCGCCGCAGCGGTTTc                      >  2:1057148/1‑139 (MQ=255)                                                                                                           cTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTGCCTTTCATCATCGCCGCAGCGGTTTCa                     >  2:120304/1‑139 (MQ=255)                                                                                                           cTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTGCCTTTCATCATCGCCGCAGCGGTTTCa                     >  1:872251/1‑139 (MQ=255)                                                                                                           cTGCCATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTGCCTTTCATCATCGCCGCAGCGGTTTCa                     >  2:406469/1‑139 (MQ=255)                                                                                                              ccATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTGCCTTTCATCATCGCCGCAGCGGTTTCAGTg                  <  2:1069291/139‑1 (MQ=255)                                                                                                              ccATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTGCCTTTCATCATCGCCGCAGCGGTTTCAGTg                  <  2:872251/139‑1 (MQ=255)                                                                                                               cATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTGCCTTTCATCATCGCCGCAg                             >  1:740058/1‑127 (MQ=255)                                                                                                               cATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTGCCTTTCATCATCGCCGCAg                             <  2:740058/127‑1 (MQ=255)                                                                                                               cATACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTGCCTTTCATCATCGCCGCAGCGGTTTCAGTgg                 >  1:130489/1‑139 (MQ=255)                                                                                                                 tACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTGCCTTTCATCATCGCCGCAGCGGTTTCAGTGGAc               >  1:1422392/1‑139 (MQ=255)                                                                                                                 tACATCAAAGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTGCCTTTCATCATCGCCGCAGCGGTTTCAGTGGAc               >  2:1120957/1‑139 (MQ=255)                                                                                                                        aaGAACCAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTGCCTTTCATCATCGCCGCAGCGGTTTCAGTGGACGCCACGa        <  1:1120957/139‑1 (MQ=255)                                                                                                                             ccAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTGCCTTTCATCATCGCCGCAGCGGTTTCAGTGGACGCCACGATACCg   <  2:687946/139‑1 (MQ=255)                                                                                                                              cAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGa                                                               >  1:29938/1‑78 (MQ=255)                                                                                                                              cAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGa                                                               <  2:29938/78‑1 (MQ=255)                                                                                                                              cAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTg                                                <  2:595496/93‑1 (MQ=255)                                                                                                                              cAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTg                                                >  1:595496/1‑93 (MQ=255)                                                                                                                              cAGCTATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTGCCTTTCATCATCGCCGCAGCGGTTTCAGTGGACGCCACGATACCGt  >  2:1115131/1‑139 (MQ=255)                                                                                                                                  |                                                                                                                                       CTTTGATCGGGTCAAGATACATGTGCTCGTTATCGATGTTTTTGAAGCCGTGCCAGGTGCTGTCAGAACGCAGCGGCCAGCATTCAGTCGTATCGATATGATCCGGCTGCCATACATCAAAGAACCAGCCATCAGATTCCGTTCTCAGACGTTTGATCTCTTTACGGAATTTGATCGCACGTTCAATAGAACCGTTGATCAGACGCTTACCTGCATTGCCTTTCATCATCGCCGCAGCGGTTTCAGTGGACGCCACGATACCGT  >  NC_000913/4357147‑4357410

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑