Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	AM260479	3,403,755	+C	coding (63/996 nt)	phcA ←	transcriptional regulator, LysR‑family

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AM260479	3,403,755	1	.	C	100.0%	177.5 / NA	45	A21A (GCC→GCG)	phcA	transcriptional regulator, LysR‑family
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (21/24);  total (21/24)

CACGCGGCGTTGGCGTCAGGCCATGCGGGACGCGGATGAAGAGCGGATCGTCAAAGATTTCACGCAGCCTGCCCAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTG‑GCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCAGGCCTCGGTCAGATTATTCTTAGCTAGATGGCCCCACCACTTGCACTGGCTGCAC  >  AM260479/3403628‑3403877                                                                                                                                 |                                                                                                                           cACGCGGCGTTGGCGTCAGGCCATGCGGGACGCGGATGAAGAGCGGATCGTCAAAGATTTCACGCAGCCTGCCCAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCAtt                                                                                                                       <  1:453792/134‑1 (MQ=255) cACGCGGCGTTGGCGTCAGGCCATGCGGGACGCGGATGAAGAGCGGATCGTCAAAGATTTCACGCAGCCTGCCCAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCAtt                                                                                                                       <  1:851151/134‑1 (MQ=255) cACGCGGCGTTGGCGTCAGGCCATGCGGGACGCGGATGAAGAGCGGATCGTCAAAGATTTCACGCAGCCTGCCCAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCAtt                                                                                                                       <  1:48079/134‑1 (MQ=255) cACGCGGCGTTGGCGTCAGGCCATGCGGGACGCGGATGAAGAGCGGATCGTCAAAGATTTCACGCAGCCTGCCCAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCAtt                                                                                                                       <  2:63380/134‑1 (MQ=255) cACGCGGCGTTGGCGTCAGGCCATGCGGGACGCGGATGAAGAGCGGATCGTCAAAGATTTCACGCAGCCTGCCCAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCAtt                                                                                                                       <  2:707176/134‑1 (MQ=255)         gTTGGCGTCAGGCCATGCGGGACGCGGATGAAGAGCGGATCGTCAAAGATTTCACGCAGCCTGCCCAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCATTTCGCTTGc                                                                                                               <  2:529724/134‑1 (MQ=255)                                    aTGAAGAGCGGATCGTCAAAGATTTCACGCAGCCTGCCCAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCAtt                                                                                                                       <  2:66633/99‑1 (MQ=255)                                    aTGAAGAGCGGATCGTCAAAGATTTCACGCAGCCTGCCCAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCAtt                                                                                                                       >  1:66633/1‑99 (MQ=255)                                                tCGTCAAAGATTTCACGCAGCCTGCCCAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCtt                                                                                >  1:143962/1‑126 (MQ=255)                                                tCGTCAAAGATTTCACGCAGCCTGCCCAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCtt                                                                                <  2:143962/126‑1 (MQ=255)                                                  gTCAAAGATTTCACGCAGCCTGCCCAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCAtt                                                                                                                       >  1:1038338/1‑85 (MQ=255)                                                  gTCAAAGATTTCACGCAGCCTGCCCAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCAtt                                                                                                                       <  2:1038338/85‑1 (MQ=255)                                                  gTCAAAGATTTCACGCAGCCTGCCCAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACg                                                                      >  2:348407/1‑134 (MQ=255)                                                               cGCAGCCTGCCCAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCa                                                         <  2:125842/134‑1 (MQ=255)                                                                 cAGCCTGCCCAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCAgg                                                       >  1:329072/1‑134 (MQ=255)                                                                        cccAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCa                                                         >  1:1056801/1‑125 (MQ=255)                                                                        cccAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCa                                                         <  2:1056801/125‑1 (MQ=255)                                                                                     aTACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCAGGCCTCGGTCAGATTATTCt                                     >  2:94101/1‑132 (MQ=255)                                                                                         ggCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCa                                                         >  2:575114/1‑108 (MQ=255)                                                                                         ggCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCa                                                         <  1:575114/108‑1 (MQ=255)                                                                                                  ggTCATATGCATCTTTTCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCAGGCCTCGGTCAGATTATTCTTAGCTAGATgg                          <  1:1035180/130‑1 (MQ=255)                                                                                                  ggTCATATGCATCTTTTCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCAGGCCTCGGTCAGATTATTCTTAGCTAGATgg                          >  2:1035180/1‑130 (MQ=255)                                                                                                       tatGCATCTTTTCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCAt                                                              >  2:487000/1‑89 (MQ=255)                                                                                                       tatGCATCTTTTCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCAt                                                              <  1:487000/89‑1 (MQ=255)                                                                                                             tCTTTTCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGtt                                                                    >  2:238638/1‑77 (MQ=255)                                                                                                             tCTTTTCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGtt                                                                    <  1:238638/77‑1 (MQ=255)                                                                                                                  tCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGt                                                                                                  >  2:774434/1‑42 (MQ=255)                                                                                                                  tCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGt                                                                                                  <  1:774434/42‑1 (MQ=255)                                                                                                                  tCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTaaaa                                                                                    >  1:141522/1‑56 (MQ=255)                                                                                                                  tCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTaaaa                                                                                    <  2:141522/56‑1 (MQ=255)                                                                                                                  tCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCt                                                                         >  2:884727/1‑67 (MQ=255)                                                                                                                  tCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCt                                                                         <  1:884727/67‑1 (MQ=255)                                                                                                                  tCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATc                                                          <  2:232245/82‑1 (MQ=255)                                                                                                                  tCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATc                                                          >  1:232245/1‑82 (MQ=255)                                                                                                                  tCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCAGGCCTCGGTCAGATTATTCTTAGc                                 >  2:1029966/1‑107 (MQ=255)                                                                                                                  tCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCAGGCCTCGGTCAGATTATTCTTAGc                                 <  1:1029966/107‑1 (MQ=255)                                                                                                                  tCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCAGGCCTCGGTCAGATTATTCTTAGCTAGATgg                          <  1:681174/114‑1 (MQ=255)                                                                                                                  tCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCAGGCCTCGGTCAGATTATTCTTAGCTAGATgg                          >  2:681174/1‑114 (MQ=255)                                                                                                                  tCCGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCAGGCCTCGGTCAGATTATTCTTAGCTAGATGGCCCCACCACTTGCACTGGCt      >  1:986504/1‑134 (MQ=255)                                                                                                                    cGCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCAGGCCTCGGTCAGATTATTCTTAGCTAGATGGCCCCACCACTTGCACTGGCTGc    <  1:94101/134‑1 (MQ=255)                                                                                                                     gCTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCAGGCCTCGGTCAGATTATTCTTAGCTAGATGGCCCCACCACTTGCACTGGCTGca   >  1:608842/1‑134 (MQ=255)                                                                                                                      cTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCa                                                                                          <  1:825323/46‑1 (MQ=255)                                                                                                                      cTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCa                                                                                          >  2:825323/1‑46 (MQ=255)                                                                                                                      cTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCAGGCCTCGGTCAGATTATTCTTAGCTAGATGGCCCCACCACTTGCACTGGCTGcac  <  2:329072/134‑1 (MQ=255)                                                                                                                      cTACATAAGTGCGCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCAGGCCTCGGTCAGATTATTCTTAGCTAGATGGCCCCACCACTTGCACTGGCTGca   >  1:913709/1‑133 (MQ=255)                                                                                                                                 |                                                                                                                           CACGCGGCGTTGGCGTCAGGCCATGCGGGACGCGGATGAAGAGCGGATCGTCAAAGATTTCACGCAGCCTGCCCAGCGAGTGCGATACGGCCGGTGCGGTCATATGCATCTTTTCCGCTACATAAGTG‑GCATTTCGCTTGCTCAGTAGTTCGGTGAAGATCACTAAAAGCTTCGTGTCTACGTTCACCATGATCAGGCCTCGGTCAGATTATTCTTAGCTAGATGGCCCCACCACTTGCACTGGCTGCAC  >  AM260479/3403628‑3403877

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