Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,322,651	A→G	pseudogene (631/839 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	4,322,651	0	A	G	100.0%	99.6 / NA	29	pseudogene (631/839 nt)	phnE	phosphonate ABC transporter membrane subunit
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (12/17);  total (12/17)

TCAGGGCGCAGGTTTGTTGGAACTGGAAACC‑GCGAATCGCTTCCCACAGGGTGACGCCGATCCCGCCTGCGCCGACCATGCCGACGACGGTCGCCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCAGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGT  >  NC_000913/4322514‑4322787                                                                                                                                           |                                                                                                                                         tCAGGGCGCAGGTTTGTTGGAACTGGAAACC‑GCGAATCGCTTCCCACAGGGTGACGCCGATCCCGCCTGCGCCGACCATGCCGACGACGGTCGCCGAGCGGACGTTGGGTTCGAAGCGATAGAGGGAGTAGGAGATcggc                                                                                                                                        >  2:336881/1‑140 (MQ=255) tCAGGGCGCAGGTTTGTTGGAACTGGAAACC‑GCGAATCGCTTCCCACAGGGTGACGCCGATCCCGCCTGCGCCGACCATGCCGACGACGGTCGCCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATcggc                                                                                                                                        >  2:826141/1‑140 (MQ=255)        gcAGGTTTGTTGGAAGGGTAAACC‑GGGAATCCCTTCCCACAGGGTGAGGCCGATCCCGCCTGCGCCGACCATGCCGACGACGGTCGCCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCGGCAGTGGCa                                                                                                                                 <  1:81417/140‑1 (MQ=255)                       cTGGAACCC‑GCGAATCGTTTCCCACAGGGTGCCGCTGATACCGCCTGCGCCGACCATGCCGACGACGGTCGCCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCGGCAGTGGCATCACCTGTGgcagca                                                                                                                  <  2:248117/140‑1 (MQ=255)                        tGGAAACCTGGGATTCGCTTCCCACAGGGTGTCCCCGTCACCGCCTGCCCCGACCATGCCGACGACGGTCGCCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCGGCAGTGGCATCACCTGTGgcagca                                                                                                                  <  2:403121/140‑1 (MQ=255)                               c‑gcgAATCGCTTCCCACAGGGTGACGCCGATCCCGCCTGCGCCGACCATGCCGACGACGGTCGCCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTag                                                                                                          >  2:409008/1‑140 (MQ=255)                                   gAATCGCTTCCCACAGGGTGACGCCGATCCCGCCTGCGCCGACCATGCCGACGACGGTCGCCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAgg                                                                                                       <  1:583103/140‑1 (MQ=255)                                              cacaGGGTGACGCCGATCCCGCCTGCGCCGACCATGCCGACGACGGTCGCCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAg                                                                                            <  2:202231/140‑1 (MQ=255)                                                    gTGACGCCGATCCCGCCTGCGCCGACCATGCCGACGACGGTCGCCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCttgtt                                                                                      <  1:154496/140‑1 (MQ=255)                                                             aTCCCGCCTGCGCCGACCATGCCGACGACGGTCGCCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCg                                                                               >  2:740226/1‑138 (MQ=255)                                                             aTCCCGCCTGCGCCGACCATGCCGACGACGGTCGCCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCg                                                                               <  1:740226/138‑1 (MQ=255)                                                                    cTGCGCCGACCATGCCGACGACGGTCGCCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGa                                                                      <  2:723226/140‑1 (MQ=255)                                                                                 gCCGACGACGGTCGCCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCAccg                                                         >  2:85585/1‑140 (MQ=255)                                                                                   cgacgaCGGTCGCCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCAccggg                                                       <  1:826141/140‑1 (MQ=255)                                                                                     acgacgGTCGCCGAGTGGACGTTGGCTTCCAAGCGATGGAGGGAGTAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCAccgggcc                                                     <  1:336881/140‑1 (MQ=255)                                                                                      cgacgGTCGCCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCAccgggccg                                                    <  1:39245/140‑1 (MQ=255)                                                                                              gCCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAAt                                            <  2:50904/140‑1 (MQ=255)                                                                                              gCCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAAt                                            <  1:85585/140‑1 (MQ=255)                                                                                                                 cGAAGCGATAGAGGGAGTAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCGTCCCCCGAGCCGGGCTCAATCACTTCCACCGCTTCGGaa                         >  2:269339/1‑140 (MQ=255)                                                                                                                            agGGAGTAGGAGATCGGAAGTGTCATCACCTTTGGCAGCCCGCCGTAGTGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGga              <  2:229111/140‑1 (MQ=255)                                                                                                                                aGTAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGc          >  1:151246/1‑140 (MQ=255)                                                                                                                                 gTAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCa         <  2:689681/140‑1 (MQ=255)                                                                                                                                  tAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTGAATAGATTCCACCGCTGCGGACAGCAGCTTGGAGAGCAc        >  2:351486/1‑140 (MQ=255)                                                                                                                                  tAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGagag           >  1:517786/1‑137 (MQ=255)                                                                                                                                  tAGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGagag           <  2:517786/137‑1 (MQ=255)                                                                                                                                   aGGAGATCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCTCCGTTTGGGAAAGGAGCTTGGAGAGCACg       >  1:231753/1‑140 (MQ=255)                                                                                                                                      agaTCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGGTTCCACCGCTTGGGAAAGCAGCTTGGAGAGCACGCCg    >  1:229111/1‑140 (MQ=255)                                                                                                                                        aTCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGc      <  1:770473/136‑1 (MQ=255)                                                                                                                                        aTCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGc      >  2:770473/1‑136 (MQ=255)                                                                                                                                        aTCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCggt  >  2:702435/1‑140 (MQ=255)                                                                                                                                        aTCGGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTCCCACCGCCTCGGAACGCAGCTCGGAGAGCACGCCggt  >  1:296898/1‑140 (MQ=255)                                                                                                                                           |                                                                                                                                         TCAGGGCGCAGGTTTGTTGGAACTGGAAACC‑GCGAATCGCTTCCCACAGGGTGACGCCGATCCCGCCTGCGCCGACCATGCCGACGACGGTCGCCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCAGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGT  >  NC_000913/4322514‑4322787

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑