Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	AM260479	3,998,635	+C	intergenic (‑221/+527)	h16_A3705 ← / ← h16_A3706	transcriptional regulator, LysR‑family/conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AM260479	3,998,633	1	.	C	100.0%	175.5 / NA	45	intergenic (‑219/+529)	h16_A3705/h16_A3706	transcriptional regulator, LysR‑family/conserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (22/23);  total (22/23)

TATTGATATGAGGGAAATGCCTAATATCTAGCCATCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACG‑CCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTCGATCCGTACAC  >  AM260479/3998505‑3998750                                                                                                                                  |                                                                                                                      tattGATATGAGGGAAATGCCTAATATCTAGCCATCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACG‑ccct                                                                                                                   >  2:963547/1‑131 (MQ=255)     gATATGAGGGAAATGCCTAATATCTAGCCATCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCg                                                                                                               >  2:140884/1‑134 (MQ=255)      atatGAGGGAAATGCCTAATATCTAGCCATCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGc                                                                                                              >  1:880991/1‑134 (MQ=255)                           tCTAGCCATCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTcgccgccg                                                                                          <  1:832904/133‑1 (MQ=255)                               gCCATCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTg                                                                                     <  1:395726/134‑1 (MQ=255)                                ccATCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGt                                                                                    <  1:963547/134‑1 (MQ=255)                                  aTCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCg                                                                                  >  2:1066908/1‑134 (MQ=255)                                  aTCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCg                                                                                  >  1:1060452/1‑134 (MQ=255)                                  aTCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCg                                                                                  >  1:1137900/1‑134 (MQ=255)                                     ggATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGcc                                                                               <  2:880991/134‑1 (MQ=255)                                     ggATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGcc                                                                               <  2:70484/134‑1 (MQ=255)                                             cAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGc                                                                       >  1:475072/1‑134 (MQ=255)                                                         gTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGa                                                            <  1:140884/133‑1 (MQ=255)                                                         gTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGa                                                            <  2:299522/133‑1 (MQ=255)                                                              tcgtcgAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGc                                                       >  1:3246/1‑133 (MQ=255)                                                                gtcgAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGc                                                                                >  1:3063/1‑106 (MQ=255)                                                                gtcgAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGc                                                                                <  2:3063/106‑1 (MQ=255)                                                                gtcgAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGcc                                                                >  2:553354/1‑122 (MQ=255)                                                                gtcgAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGcc                                                                <  1:553354/122‑1 (MQ=255)                                                                gtcgAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAg                                                    >  2:935786/1‑134 (MQ=255)                                                                gtcgAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAg                                                    >  2:564061/1‑134 (MQ=255)                                                                gtcgAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAg                                                    <  2:3246/134‑1 (MQ=255)                                                                   gAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTc                                                 >  1:896513/1‑134 (MQ=255)                                                                   gAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTc                                                 <  1:1066908/134‑1 (MQ=255)                                                                             cTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCa                                       <  1:708051/134‑1 (MQ=255)                                                                                           cAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAg                         >  2:943492/1‑134 (MQ=255)                                                                                            aaTAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAgg                        <  1:1184690/134‑1 (MQ=255)                                                                                                gagaAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCAc                                                                           >  2:412639/1‑79 (MQ=255)                                                                                                gagaAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCAc                                                                           <  1:412639/79‑1 (MQ=255)                                                                                                  gaAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCa                                                                                                      <  2:937122/50‑1 (MQ=39)                                                                                                  gaAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCa                                                                                                      >  1:937122/1‑50 (MQ=39)                                                                                                  gaAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCAc                                      >  2:50855/1‑114 (MQ=255)                                                                                                  gaAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCAc                                      <  1:50855/114‑1 (MQ=255)                                                                                                   aaaGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCaa                 <  1:935786/134‑1 (MQ=255)                                                                                                   aaaGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCaa                 <  2:1060452/134‑1 (MQ=255)                                                                                                     aGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGt               <  1:564061/134‑1 (MQ=255)                                                                                                       ccTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTc             >  2:310082/1‑134 (MQ=255)                                                                                                       ccTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTc             <  2:1137900/134‑1 (MQ=255)                                                                                                       ccTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTc             <  1:310082/134‑1 (MQ=255)                                                                                                         tGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTCGa           >  1:968027/1‑134 (MQ=255)                                                                                                          gAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTCGAt          >  2:417172/1‑134 (MQ=255)                                                                                                            aTCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCaa                 <  2:161525/125‑1 (MQ=255)                                                                                                            aTCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCaa                 >  1:161525/1‑125 (MQ=255)                                                                                                              cATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTCGATCCg       >  1:324376/1‑133 (MQ=255)                                                                                                               aTGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTCGATCCGTa     >  1:1049302/1‑134 (MQ=255)                                                                                                                  aaaaCCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTCGATCCGTacac  <  2:475072/134‑1 (MQ=255)                                                                                                                                  |                                                                                                                      TATTGATATGAGGGAAATGCCTAATATCTAGCCATCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACG‑CCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTCGATCCGTACAC  >  AM260479/3998505‑3998750

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑