Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	402,089	(A)7→8	coding (343/1416 nt)	phoA →	alkaline phosphatase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	402,082	1	.	A	100.0%	182.7 / NA	51	N112K (AAT→AAA)	phoA	alkaline phosphatase
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base A (31/20);  total (31/20)

TGATTGGCGATGGGATGGGGGACTCGGAAATTACTGCCGCACGTAATTATGCCGAAGGTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAAT‑AAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAA  >  NC_000913/401955‑402215                                                                                                                                 |                                                                                                                                       tGATTGGCGATGGGATGGGGGACTCGGAAATTACTGCCGCACGTAATTATGCCGAAGGTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAAT‑aaaaaaaaccgg                                                                                                                            <  1:1137758/140‑6 (MQ=255)            gggatgggGGACTCGGAAATTACTGCCGCACGTAATTATGCCGAAGGTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACt                                                                                                                 <  1:62196/140‑1 (MQ=255)                      aCTCGGAAATTACTGCCGCACGTAATTATGCCGAAGGTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCAGCAAACCGGACTACGTCACCGa                                                                                                       >  2:196666/1‑140 (MQ=255)                       cTCGGAAATTACTGCCGCACGTAATTATGCCGAAGGTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGAc                                                                                                      >  1:706923/1‑140 (MQ=255)                        tCGGAAATTACTGCCGCACGTAATTATGCCGAAGGTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACt                                                                                                     >  1:374149/1‑140 (MQ=255)                          ggAAATTACTGCCGCACGTAATTATGCCGAAGGTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCg                                                                                                   >  1:927061/1‑140 (MQ=255)                           gAAATTACTGCCGCACGTAATTATGCCGAAGGTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCgg                                                                                                  <  2:998182/140‑1 (MQ=255)                                          cGTAATTATGCCGAAGGTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCg                                                                                   >  1:556804/1‑140 (MQ=255)                                           gTAATTATGCCGAAGGTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGc                                                                                  <  2:672814/140‑1 (MQ=255)                                                    ccGAAGGTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGc                                                                                        <  1:1065069/125‑1 (MQ=255)                                                    ccGAAGGTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGc                                                                                        >  2:1065069/1‑125 (MQ=255)                                                    ccGAAGGTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAAc                                                                         >  1:353773/1‑140 (MQ=255)                                                     cGAAGGTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAAcc                                                                        >  1:726577/1‑140 (MQ=255)                                                     cGAAGGTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAAcc                                                                        >  2:104703/1‑140 (MQ=255)                                                      gAAGGTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAACCCGGACTACGTCCCCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCg                                                                       <  2:831129/140‑1 (MQ=255)                                                         ggTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGTGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGgtg                                                                    >  2:159696/1‑140 (MQ=255)                                                            gcgggcggCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGTGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCa                                                                 <  1:159696/140‑1 (MQ=255)                                                            gcgggcggCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCa                                                                 <  2:374149/140‑1 (MQ=255)                                                                        tttAAGGGTATAGACCCCTACCCGTTCCCCGGGCAATACCCCCCTTTGGCGCGAAAA‑AAAAAAACCCGGCAACCCGGCCTCCGCCACCGCCCCGGCGGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACg                                                     <  2:1150567/140‑1 (MQ=255)                                                                        tttAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACg                                                     <  1:104703/140‑1 (MQ=255)                                                                             aGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGgcgcg                                                <  2:726577/140‑1 (MQ=255)                                                                              ggTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGgcgcgc                                               >  1:923273/1‑140 (MQ=255)                                                                              ggTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGgcgcgc                                               >  2:446973/1‑140 (MQ=255)                                                                              ggTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGgcgcgc                                               >  1:13255/1‑140 (MQ=255)                                                                              ggTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGgcgcgc                                               >  1:665011/1‑140 (MQ=255)                                                                               gTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCt                                              <  2:665011/140‑1 (MQ=255)                                                                               gTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCt                                              <  1:446973/140‑1 (MQ=255)                                                                                  taGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTggg                                           <  1:303429/140‑1 (MQ=255)                                                                                         cttaccgcttaccgGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGgcgcgc                                               >  2:98732/1‑129 (MQ=255)                                                                                         cttaccgcttaccgGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGgcgcgc                                               <  1:98732/129‑1 (MQ=255)                                                                                         cttaccgcttaccgGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCt                                              <  1:968556/130‑1 (MQ=255)                                                                                         cttaccgcttaccgGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCt                                              >  2:968556/1‑130 (MQ=255)                                                                                         cttaccgcttaccgGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGat                                    >  1:931919/1‑140 (MQ=255)                                                                                          ttaccgcttaccgGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTg                                             >  2:713927/1‑130 (MQ=255)                                                                                          ttaccgcttaccgGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTg                                             <  1:713927/130‑1 (MQ=255)                                                                                                  taccgGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTggg                                           >  1:621433/1‑124 (MQ=255)                                                                                                  taccgGGCAATACACTCACTATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTggg                                           <  2:621433/124‑1 (MQ=255)                                                                                                               actcactATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCaa              <  2:1096145/140‑1 (MQ=255)                                                                                                                  cactATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATTTTCACGAAAAAGATCACCCAACGa           >  2:1033116/1‑140 (MQ=255)                                                                                                                  cactATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGa           >  2:181007/1‑140 (MQ=255)                                                                                                                   actATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGAt          >  2:913607/1‑140 (MQ=255)                                                                                                                   actATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGAt          >  2:899071/1‑140 (MQ=255)                                                                                                                   actATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGAt          >  2:1132984/1‑140 (MQ=255)                                                                                                                   actATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGAt          >  2:742739/1‑140 (MQ=255)                                                                                                                    ctATGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGAtt         <  1:899071/140‑1 (MQ=255)                                                                                                                      aTGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCaa              <  2:111177/133‑1 (MQ=255)                                                                                                                      aTGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCaa              >  2:697488/1‑133 (MQ=255)                                                                                                                      aTGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCaa              >  1:111177/1‑133 (MQ=255)                                                                                                                      aTGCGCTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCaa              <  1:697488/133‑1 (MQ=255)                                                                                                                         cgcTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGa    >  2:914237/1‑140 (MQ=255)                                                                                                                           cTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGaaa  >  2:977289/1‑140 (MQ=255)                                                                                                                           cTGAATAAAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGaaa  >  1:60990/1‑140 (MQ=255)                                                                                                                           cTGAATAAAAAAAA‑CCGACAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGaaa  >  2:278417/1‑140 (MQ=255)                                                                                                                                 |                                                                                                                                       TGATTGGCGATGGGATGGGGGACTCGGAAATTACTGCCGCACGTAATTATGCCGAAGGTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAAT‑AAAAAAA‑CCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAA  >  NC_000913/401955‑402215

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑