Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,325,152	A→G	I5T (ATC→ACC)	phnC ←	phosphonate ABC transporter ATPase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,325,152	0	A	G	100.0%	218.8 / NA	61	I5T (ATC→ACC)	phnC	phosphonate ABC transporter ATPase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (30/31);  total (30/31)

GACGTAAAAGGGTGGATTTTCCGGAACCCGACGGCCCAAGCAGAGCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGATAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTAAAAGTGACTAACAGATGAAGAGTTAACGGGAATTCGAT  >  NC_000913/4325021‑4325266                                                                                                                                    |                                                                                                                   gACGTAAAAGGGTGGATTTTCCGGAACCCGACGGCCCAAGCAGAGCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGt                                                                                                             <  1:410255/139‑1 (MQ=255)  aCGTAAAAGGGTGGATTTTCCGGAACCCGACGGCCCAAGCAGAGCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGtt                                                                                                            >  2:936434/1‑139 (MQ=255)      aaaaGGGTGGATTTTCCGGAACCCGACGGCCCAAGCAGAGCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCa                                                                                                        <  1:971608/139‑1 (MQ=255)            gTGGATTTTCCGGAACCCGACGGCCCAAGCAGAGCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGc                                                                                                  >  2:334683/1‑139 (MQ=255)             tGGATTTTCCGGAACCCGACGGCCCAAGCAGAGCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCa                                                                                                 <  2:870046/139‑1 (MQ=255)              ggATTTTCCGGAACCCGACGGCCCAAGCAGAGCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAg                                                                                                >  2:879366/1‑139 (MQ=255)              ggATTTTCCGGAACCCGACGGCCCAAGCAGAGCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAg                                                                                                >  2:897039/1‑139 (MQ=255)              ggATTTTCCGGAACCCGACGGCCCAAGCAGAGCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAg                                                                                                >  1:834273/1‑139 (MQ=255)               gATTTTCCGGAACCCGACGGCCCAAGCAGAGCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGc                                                                                               >  2:795657/1‑139 (MQ=255)               gATTTTCCGGAACCCGACGGCCCAAGCAGAGCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGc                                                                                               <  1:1341368/139‑1 (MQ=255)               gATTTTCCGGAACCCGACGGCCCAAGCAGAGCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGc                                                                                               <  1:1511888/139‑1 (MQ=255)               gATTTTCCGGAACCCGACGGCCCAAGCAGAGCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGc                                                                                               <  2:353978/139‑1 (MQ=255)               gATTTTCCGGAACCCGACGGCCCAAGCAGAGCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGc                                                                                               <  1:334683/139‑1 (MQ=255)                aTTTTCCGGAACCCGACGGCCCAAGCAGAGCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGcc                                                                                              >  2:1287255/1‑139 (MQ=255)                                      aaGCAGAGCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCt                                                                                             <  1:1058987/118‑1 (MQ=255)                                      aaGCAGAGCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCt                                                                                             >  2:1058987/1‑118 (MQ=255)                                           gagCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGc                                                                   >  1:299422/1‑139 (MQ=255)                                            agCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCg                                                                  <  2:299422/139‑1 (MQ=255)                                             gCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCgg                                                                 >  1:468197/1‑139 (MQ=255)                                              ccaccaTTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGa                                                                <  1:1287255/139‑1 (MQ=255)                                                 ccaTTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAg                                                                                  >  1:411568/1‑118 (MQ=255)                                                 ccaTTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAg                                                                                  <  2:411568/118‑1 (MQ=255)                                                     ttCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATtgt                                                         <  2:1289331/139‑1 (MQ=255)                                                      tCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCg                                                                  >  2:1494773/1‑129 (MQ=255)                                                      tCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCg                                                                  <  1:1494773/129‑1 (MQ=255)                                                        aCCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCa                                                                          <  2:335245/119‑1 (MQ=255)                                                        aCCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCa                                                                          >  1:335245/1‑119 (MQ=255)                                                              atgaATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAG‑GGCTCCATCGTGGCGGATTATTGTGACGATTTgg                                               <  1:879366/139‑1 (MQ=255)                                                                        aGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTaaa                                      >  2:392906/1‑139 (MQ=255)                                                                         gATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTaaaa                                     >  2:1320758/1‑139 (MQ=255)                                                                           tCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTAAAAGt                                   >  2:872829/1‑139 (MQ=255)                                                                             aaCCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGc                                                                                               <  2:709100/77‑1 (MQ=255)                                                                             aaCCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGc                                                                                               >  1:709100/1‑77 (MQ=255)                                                                             aaCCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTAAAAGTGa                                 >  2:795246/1‑139 (MQ=255)                                                                              aCCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTAAAAGTGAc                                >  1:520856/1‑139 (MQ=255)                                                                               ccGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGc                                                                                               <  2:1396788/75‑1 (MQ=255)                                                                               ccGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGc                                                                                               >  1:1396788/1‑75 (MQ=255)                                                                               ccGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTAAAAGTGACt                               <  1:795246/139‑1 (MQ=255)                                                                               ccGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTAAAAGTGACt                               >  2:1323390/1‑139 (MQ=255)                                                                                 gCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTAAAAGTGACTaa                             <  1:1323390/139‑1 (MQ=255)                                                                                  cATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGc                                                                                               >  2:650165/1‑72 (MQ=255)                                                                                  cATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGc                                                                                               <  1:650165/72‑1 (MQ=255)                                                                                  cATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTAAAAGTGACTAAc                            <  2:1657853/139‑1 (MQ=255)                                                                                    tGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCg                                                                  >  2:202017/1‑99 (MQ=255)                                                                                    tGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCg                                                                  <  1:202017/99‑1 (MQ=255)                                                                                    tGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATtgt                                                         >  2:1306802/1‑108 (MQ=255)                                                                                    tGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATtgt                                                         <  1:1306802/108‑1 (MQ=255)                                                                                    tGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTAAAAGTGACt                               <  1:1332592/134‑1 (MQ=255)                                                                                    tGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTAAAAGTGACt                               >  2:1332592/1‑134 (MQ=255)                                                                                    tGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTAAAAGTGACTAACAg                          >  1:610138/1‑139 (MQ=255)                                                                                       aGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTAAAAGTGACTAACAGATg                       <  2:834273/139‑1 (MQ=255)                                                                                                    gATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTAAAAGTGACTAACAGATGAAGAGTTAACggg          <  1:897039/139‑1 (MQ=255)                                                                                                    gATTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTAAAAGTGACTAACAGATGAAGAGTTAACggg          <  2:1454903/139‑1 (MQ=255)                                                                                                     aTTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGc                                                                                               <  1:937832/53‑1 (MQ=255)                                                                                                     aTTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGc                                                                                               >  2:937832/1‑53 (MQ=255)                                                                                                     aTTGAAGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTAAAAGTGACTAACAGATGAAGAGTTAACGGGa         >  2:563184/1‑139 (MQ=255)                                                                                                         aaGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGa                                                                >  2:1118160/1‑80 (MQ=255)                                                                                                         aaGGTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGa                                                                <  1:1118160/80‑1 (MQ=255)                                                                                                            gTTTTGGCGAGCTTCTCGACACGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTAAAAGTGACTAACAGATGAAGAGTTAACGGGAATTCGAt  <  1:795657/139‑1 (MQ=255)                                                                                                                                 cGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTgg                                               >  2:857144/1‑73 (MQ=255)                                                                                                                                 cGGGTAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTgg                                               <  1:857144/73‑1 (MQ=255)                                                                                                                                    |                                                                                                                   GACGTAAAAGGGTGGATTTTCCGGAACCCGACGGCCCAAGCAGAGCCACCATTTCACCGTGATGAATGTTCAGATCAACCGCATGCAGCGCCTGATGCTGATTGAAGGTTTTGGCGAGCTTCTCGACACGGATAATCGTTTGCATGATGCAGCCTCCCTAAAAAAGTGGCTCCATCGTGGCGGATTATTGTGACGATTTGGTTAATTAAAAGTGACTAACAGATGAAGAGTTAACGGGAATTCGAT  >  NC_000913/4325021‑4325266

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑