Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,323,211	Δ1 bp	pseudogene (71/839 nt)	phnE ←	phosphonate ABC transporter membrane subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,323,208	0	G	.	100.0%	139.9 / NA	33	pseudogene (74/839 nt)	phnE	phosphonate ABC transporter membrane subunit
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (16/17);  total (16/17)

GCGGCGAACGTCGCCATGTTGCCGCCGTCTTTGATCAGCGTAAGCGGGGCCATTTCCGCGCCCTGCCACGAGACGACCAACACGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGTGGGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTA  >  NC_000913/4323076‑4323331                                                                                                                                     |                                                                                                                            gcggcgAACGTCGCCATGTTGCCGCCGTCTTTGATCAGCGTAAGCGGGGCCATTTCCGCGCCCTGCCACGAGACGACCAACACGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCgatg                                                                                                                     >  1:1010607/1‑140 (MQ=255)     cgAACGTCGCCATGTTGCCGCCGTCTTTGATCAGCGTAAGCGGGGCCATTTCCGCGCCCTGCCACGAGACGACCAACACGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCgatggtga                                                                                                                 <  1:1087848/140‑1 (MQ=255)             gCCATGTTGCCGCCGTCTTTGATCAGCGTAAGCGGGGCCATTTCCGCGCCCTGCCACGAGACGACCAACACGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGc                                                                                                         <  2:1010607/140‑1 (MQ=255)               cATGTTGCCGCCGTCTTTGATCAGCGTAAGCGGGGCCATTTCCGCGCCCTGCCACGAGACGACCAACACGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCAt                                                                                                       >  1:585403/1‑140 (MQ=255)                             cTTTGATCAGCGTAAGCGGGGCCATTTCCGCGCCCTGCCACGAGACGACCAACACGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTc                                                                                         <  1:449077/140‑1 (MQ=255)                              tttGATCAGCGTAAGCGGGGCCATTTCCGCGCCCTGCCACGAGACGACCAACACGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCt                                                                                        >  1:67926/1‑140 (MQ=255)                                  aTCAGCGTAAGCGGGGCCATTTCCGCGCCCTGCCACGAGACGACCAACACGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAg                                                                                    <  2:93815/140‑1 (MQ=255)                                   tCAGCGTAAGCGGGGCCATTTCCGCGCCCTGCCACGAGACGACCAACACGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAgg                                                                                   <  2:67926/140‑1 (MQ=255)                                        gTAAGCGGGGCCATTTCCGCGCCCTGCCACGAGACGACCAACACGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGa                                                                              >  1:722422/1‑140 (MQ=255)                                           aGCGGGGCCATTTCCGCGCCCTGCCACGAGACGACCAACACGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATaa                                                                           <  1:830544/140‑1 (MQ=255)                                                 gCCATTTCCGCGCCCTGCCACGAGACGACCAACACGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCt                                                                     >  1:543469/1‑140 (MQ=255)                                                 gCCATTTCCGCGCCCTGCCACGAGACGACCAACACGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCt                                                                     >  1:331401/1‑140 (MQ=255)                                                  ccATTTCCGCGCCCTGCCACGAGACGACCAACACGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCtt                                                                    <  2:543469/140‑1 (MQ=255)                                                      ttCCGCGCCCTGCCACGAGACGACCAACACGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCAc                                                                <  1:477356/140‑1 (MQ=255)                                                                   cACGAGACGACCAACACGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATc                                                   <  2:518674/140‑1 (MQ=255)                                                                             ccAACACGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGca                                         <  2:722422/140‑1 (MQ=255)                                                                                  acGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTg                                    >  2:502367/1‑140 (MQ=255)                                                                                               cGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGc                       >  2:1093470/1‑140 (MQ=255)                                                                                               cGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGc                       >  2:939549/1‑140 (MQ=255)                                                                                                       cTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCg                     >  2:439303/1‑134 (MQ=255)                                                                                                       cTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCg                     <  1:439303/134‑1 (MQ=255)                                                                                                       cTCAGAAGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGt               >  1:595424/1‑140 (MQ=255)                                                                                                            aaGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTAt          >  1:455009/1‑140 (MQ=255)                                                                                                            aaGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTAt          >  2:755662/1‑140 (MQ=255)                                                                                                             aGCGAGAACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATc         <  2:331401/140‑1 (MQ=255)                                                                                                                 agaACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCgggg                  >  1:899513/1‑127 (MQ=255)                                                                                                                 agaACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCgggg                  <  2:899513/127‑1 (MQ=255)                                                                                                                 agaACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGAc     <  2:455009/140‑1 (MQ=255)                                                                                                                 agaACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGAc     >  2:325648/1‑140 (MQ=255)                                                                                                                 agaACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGAc     <  1:325648/140‑1 (MQ=255)                                                                                                                  gaACCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGAcc    >  2:828974/1‑140 (MQ=255)                                                                                                                   aaCCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCt   <  2:97202/140‑1 (MQ=255)                                                                                                                    aCCAGCTGCGCTTGGGT‑GGGCGATGGTGATGGTTCGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTa  <  2:595424/140‑1 (MQ=255)                                                                                                                                     |                                                                                                                            GCGGCGAACGTCGCCATGTTGCCGCCGTCTTTGATCAGCGTAAGCGGGGCCATTTCCGCGCCCTGCCACGAGACGACCAACACGGCGAGTACAACGGCCCAGCTCAGAAGCGAGAACCAGCTGCGCTTGGGTGGGGCGATGGTGATGGTTTGCATGTTTGGCTCCGGTCTGTAGGCCGGATAAGGTGCTTGCACCGCATCCGGCATCAACGCCTGCACATTGTCGGATGCGACGCCGGGGCGTCTTATCCGACCTA  >  NC_000913/4323076‑4323331

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑