Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	248,122	T→C	R162R (CGT→CGC)	rayT →	RAYT REP element‑mobilizing transposase, TnpA(REP)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	248,122	0	T	C	100.0%	124.7 / NA	35	R162R (CGT→CGC)	rayT	RAYT REP element‑mobilizing transposase, TnpA(REP)
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (18/17);  total (18/17)

TCCAGTAAAGCATGGTTGGGTAAAGCAAGTGAGTGATTGGCCATTCTCAACGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGTATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCGGATCGGTAGGCCGGATAAGGCGTTTATGCCGCATCCGGCAGTTATGCGCAG  >  NC_000913/247993‑248245                                                                                                                                  |                                                                                                                            tCCAGTAAAGCATGGTTGGGTAAAGCAAGTGAGTGATTGGCCATTCTCAACGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCa                                                                                                                    >  2:991315/1‑139 (MQ=255) tCCAGTAAAGCATGGTTGGGTAAAGCAAGTGAGTGATTGGCCATTCTCAACGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCa                                                                                                                    <  2:835608/139‑1 (MQ=255)           cATGGTTGGGTAAAGCAAGTGAGTGATTGGCCATTCTCAACGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTgcg                                                                                                          >  2:851838/1‑139 (MQ=255)                ttGGGTAAAGCAAGTGAGTGATTGGCCATTCTCAACGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCa                                                                                                                         <  2:421315/119‑1 (MQ=255)                ttGGGTAAAGCAAGTGAGTGATTGGCCATTCTCAACGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCa                                                                                                                         >  1:421315/1‑119 (MQ=255)                   ggTAAAGCAAGTGAGTGATTGGCCATTCTCAACGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGcc                                                                                                  >  2:794579/1‑139 (MQ=255)                        aGCAAGTGAGTGATTGGCCATTCTCAACGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGCCTGATg                                                                                             <  2:41270/139‑1 (MQ=255)                          cAAGTGAGTGATTGGCCATTCTCAACGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCa                                                                                                                         >  2:1029476/1‑109 (MQ=255)                          cAAGTGAGTGATTGGCCATTCTCAACGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCa                                                                                                                         <  1:1029476/109‑1 (MQ=255)                             gtgagtgaTTGGCCATTCTCAACGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGCCTGATGCGACg                                                                                        >  1:160076/1‑139 (MQ=255)                              tgagtgaTTGGCCATTCTCAACGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGc                                                                                       >  2:419010/1‑139 (MQ=255)                                      tGGCCATTCTCAACGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGt                                                                               <  2:160076/139‑1 (MQ=255)                                       ggCCATTCTCAACGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTc                                                                              >  1:122289/1‑139 (MQ=255)                                            ttCTCAACGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATc                                                                         >  2:516950/1‑139 (MQ=255)                                             tctcAACGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCa                                                                        >  1:1015002/1‑139 (MQ=255)                                              ctcAACGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTCTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCAt                                                                       <  1:991315/139‑1 (MQ=255)                                                 aaCGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGcc                                                                    >  1:821173/1‑139 (MQ=255)                                                       ccATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCa                                                                                                                    >  1:416603/1‑85 (MQ=255)                                                       ccATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCa                                                                                                                    <  2:416603/85‑1 (MQ=255)                                                       ccATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACaaa                                                              >  1:91204/1‑139 (MQ=255)                                                        cATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAAc                                                             <  2:122289/139‑1 (MQ=255)                                                               aTGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAAc                                                             <  2:357455/132‑1 (MQ=255)                                                               aTGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAAc                                                             >  1:357455/1‑132 (MQ=255)                                                                tGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATc                                                                         >  1:1047316/1‑119 (MQ=255)                                                                tGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATc                                                                         <  2:1047316/119‑1 (MQ=255)                                                                             ttATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCGGATCGGTAGGCCg                                        <  1:851838/139‑1 (MQ=255)                                                                                     cATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCa                                                                                                                         <  1:886037/50‑1 (MQ=255)                                                                                     cATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCa                                                                                                                         >  2:886037/1‑50 (MQ=255)                                                                                      aTCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCa                                                                                                                         <  2:851817/49‑1 (MQ=255)                                                                                      aTCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGCATCa                                                                                                                         >  1:851817/1‑49 (MQ=255)                                                                                                   gggACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCa                                                                                                        >  2:12232/1‑53 (MQ=255)                                                                                                   gggACGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCa                                                                                                        <  1:12232/53‑1 (MQ=255)                                                                                                      aCGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCGGATCGGTAGGCCGGATAAGGCGTTTATGCCGCATCCgg               <  1:794579/139‑1 (MQ=255)                                                                                                      aCGTAACGGATTTTAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCGGATCGGTAGGCCGGATAAGGCGTTTATGCCGCATCCgg               <  2:821173/139‑1 (MQ=255)                                                                                                                   tAGTGCCGGGGAGCGCATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCGGATCGGTAGGCCGGATAAGGCGTTTATGCCGCATCCGGCAGTTATGCGCAg  <  1:516950/139‑1 (MQ=255)                                                                                                                                  |                                                                                                                            TCCAGTAAAGCATGGTTGGGTAAAGCAAGTGAGTGATTGGCCATTCTCAACGTTCCATCGCGATGTCGCGCGAGGGTTATATCCCATCGATTGGGCGGGGGACGTAACGGATTTTAGTGCCGGGGAGCGTATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCGGATCGGTAGGCCGGATAAGGCGTTTATGCCGCATCCGGCAGTTATGCGCAG  >  NC_000913/247993‑248245

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: ‑