Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,324,004	G→A	P117S (CCG→TCG)	phnD ←	phosphonate ABC transporter periplasmic binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,324,004	0	G	A	100.0%	151.4 / NA	41	P117S (CCG→TCG)	phnD	phosphonate ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (24/17);  total (24/17)

TCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGGCGCGATCCACCGCTTCCATCGCCGACAGATT  >  NC_000913/4323929‑4324079                                                                            |                                                                            tCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACg                                                                           <  2:863942/78‑1 (MQ=255)     cTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGatccatc                                                                    >  2:864003/1‑81 (MQ=255)     cTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGatccatc                                                                    >  2:863990/1‑81 (MQ=255)       tCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATccg                                                                  >  2:864017/1‑81 (MQ=255)       tCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATccg                                                                  >  1:863996/1‑81 (MQ=255)        cGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGatccatcc                                                                   <  2:863943/79‑1 (MQ=255)        cGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATccgc                                                                 >  1:864026/1‑81 (MQ=255)         gCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATccgcc                                                                >  2:863992/1‑81 (MQ=255)         gCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATccgcc                                                                <  1:863944/81‑1 (MQ=255)         gCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGAACAACACGCTCCAGTAACCCGACGATCCATccgc                                                                 <  2:863945/80‑1 (MQ=255)               agATCGTTCAGGTTGTTGATCGGACTGTCTTAGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGAcc                                                          <  2:863946/81‑1 (MQ=255)                 aTCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGt                                                        >  1:864015/1‑81 (MQ=255)                   cGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCt                                                      >  1:864010/1‑81 (MQ=255)                    gTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTg                                                     >  2:864027/1‑81 (MQ=255)                     ttCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTgg                                                    <  1:863947/81‑1 (MQ=255)                       cAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGc                                                  >  2:863995/1‑81 (MQ=255)                        aGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCg                                                 <  2:863948/81‑1 (MQ=255)                           ttgttgATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAg                                              <  2:863949/81‑1 (MQ=255)                             gttgATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGAc                                            >  1:864006/1‑81 (MQ=255)                              ttgATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGAc                                            <  2:863950/80‑1 (MQ=255)                                gATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTg                                         >  1:864005/1‑81 (MQ=255)                                 aTCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTgg                                        <  2:863951/81‑1 (MQ=255)                                  tCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGc                                       >  2:864013/1‑81 (MQ=255)                                    ggACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCa                                     >  2:864031/1‑81 (MQ=255)                                     gACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCAt                                    >  2:864001/1‑81 (MQ=255)                                                 tgACGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGGCGCGATCCa                        >  2:864029/1‑81 (MQ=255)                                                   aCGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGGCGCGATCCAcc                      <  2:863952/81‑1 (MQ=255)                                                   aCGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGGCGCGATCCAcc                      <  2:863954/81‑1 (MQ=255)                                                   aCGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGGCGCGATCCAcc                      <  1:863953/81‑1 (MQ=255)                                                   aCGATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGGCGCGATCCAcc                      >  2:864020/1‑81 (MQ=255)                                                     gATCAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGGCGCGATCCACCGc                    >  1:864016/1‑81 (MQ=255)                                                        cAACACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGGCGCGATCCACCGCTTc                 >  2:863955/1‑81 (MQ=255)                                                         aaCACGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGGCGCGATCCACCGCTTc                 <  1:863956/80‑1 (MQ=255)                                                          acacGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGGCGCGATCCACCGCTTCCa               >  2:864009/1‑81 (MQ=255)                                                            acGCTCCAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGGCGCGATCCACCGCTTCCATc             >  2:864036/1‑81 (MQ=255)                                                                  cAGTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGGCGCGATCCACCGCTTCCATCGCCg         <  2:863957/79‑1 (MQ=255)                                                                    gTAACCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGGCGCGATCCACCGCTTCCATCGCCGACAg     <  2:863958/81‑1 (MQ=255)                                                                      aaCCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGGCGCGATCCACCGCTTCCATCGCCGACAGAt   >  1:864011/1‑81 (MQ=255)                                                                      aaCCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGGCGCGATCCACCGCTTCCATCGCCGACAGAt   >  1:864019/1‑81 (MQ=255)                                                                       aCCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGGCGCGATCCACCGCTTCCATCGCCGACAGAtt  <  2:863959/81‑1 (MQ=255)                                                                       aCCCGACGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGGCGCGATCCACCGCTTCCATCGCCGACAGAtt  >  1:864028/1‑81 (MQ=255)                                                                            |                                                                            TCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGGCGCGATCCACCGCTTCCATCGCCGACAGATT  >  NC_000913/4323929‑4324079

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑