Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	1,197,502	C→T	G11R (GGA→AGA)	ymfD ←	e14 prophage; putative SAM‑dependent methyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	1,197,502	0	C	T	100.0%	147.9 / NA	44	G11R (GGA→AGA)	ymfD	e14 prophage; putative SAM‑dependent methyltransferase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (23/21);  total (23/21)

TGATTAATTCATCAGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCCGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATACCACTCAC  >  NC_000913_3_pae_tpiA/1197358‑1197643                                                                                                                                                   |                                                                                                                                              tGATTAATTCATCAGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGc                                                                                                                                           >  2:852409/1‑149 (MQ=255)   aTTAATTCATCAGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCat                                                                                                                                         >  1:828334/1‑149 (MQ=255)    ttAATTCATCAGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCata                                                                                                                                        >  1:1117831/1‑149 (MQ=255)    ttAAGTCATCAGAATATCAAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCata                                                                                                                                        <  1:14058/149‑1 (MQ=255)        ttCATCAGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTAACTCAAGGCGTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCAtattat                                                                                                                                    <  1:1415136/149‑1 (MQ=255)            tcaGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGtt                                                                                                                                >  2:314229/1‑149 (MQ=255)            tcaGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGtt                                                                                                                                >  1:1357977/1‑149 (MQ=255)            tcaGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGtt                                                                                                                                <  1:904126/149‑1 (MQ=255)                  tatCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGc                                                                                                                          <  1:77294/149‑1 (MQ=255)                     cTAAGTTTTACGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGATAAAATATCT‑AGAGGGGA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAg                                                                                                                       <  2:520432/149‑1 (MQ=255)                      tAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGt                                                                                                                      >  1:1223466/1‑149 (MQ=255)                        aGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTAc                                                                                                                    <  1:314229/149‑1 (MQ=255)                        aGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTAc                                                                                                                    <  1:932874/149‑1 (MQ=255)                                    ccAAAATCAAGGGCGTGGCCATTTTTCTCGACGCTTCTAATCTACTCGCAAAGATATCT‑ACAGGGCA‑TCGTATGAGGTTTGGCTGCATTCCCTGAGCGGATATTAACTCTGTGCATATTATACTTCTAAGCAAGTCCCATTCAATTAAt                                                                                                        <  1:1186881/149‑1 (MQ=255)                                    ccAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGGGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAAt                                                                                                        <  2:1357977/149‑1 (MQ=255)                                    ccAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTGTGAGGTTTTGCTGCATTCTCTGAGCGGATATTAACTCTGTGCATNTTATAGTACTAAGCAAGTGCCATTCAATAAAt                                                                                                        >  1:641035/1‑149 (MQ=255)                                    ccAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAAt                                                                                                        <  2:53620/149‑1 (MQ=255)                                     cAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATg                                                                                                       >  2:1012792/1‑149 (MQ=255)                                          tCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTAtt                                                                                                  >  1:1401568/1‑149 (MQ=255)                                                     gCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGaaaa                                                                                       >  1:538982/1‑149 (MQ=255)                                                     gCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGaaaa                                                                                       >  1:1150652/1‑149 (MQ=255)                                                     gCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCGGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTGAATTAATGTTATTTTTAGTGaaaa                                                                                       >  1:1208942/1‑149 (MQ=255)                                                        aTTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAAtt                                                                                    >  2:3425/1‑149 (MQ=255)                                                           tttCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTAGAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCtt                                                                                 <  1:1135448/149‑1 (MQ=255)                                                                 aaTGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCttttattt                                                                           >  2:942337/1‑149 (MQ=255)                                                                 aaTGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCttttattt                                                                           >  2:37581/1‑149 (MQ=255)                                                                       tCTAATATACTCGCAAAGATATCTAAAAGAACAGACGTA‑‑ATGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGt                                                                     >  2:1036638/1‑149 (MQ=255)                                                                          aaTGTACTCGCAATGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCg                                                                  <  2:1245543/149‑1 (MQ=255)                                                                             ataCTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGTATTGTCTGAGTGTGTATTAACTCTGTGCATATTATAGTTCAAAGCAAGTGCTATTAAATTTATGTTATTTTTAGTGAAAAATTTTTTTATTTTATCGTCCGGGa                                                               >  2:1096083/1‑149 (MQ=255)                                                                                    cAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTACGGTATTTTTcc                                                        >  2:818881/1‑149 (MQ=255)                                                                                       aGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCgac                                                     <  2:538982/149‑1 (MQ=255)                                                                                         atatCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCgactt                                                   >  2:606300/1‑149 (MQ=255)                                                                                                 gagGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTc                                            <  1:37581/149‑1 (MQ=255)                                                                                                    ggCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATtata                                                                                                                                   >  1:1195899/1‑59 (MQ=255)                                                                                                    ggCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATtata                                                                                                                                   <  2:1195899/59‑1 (MQ=255)                                                                                                         tCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTg                                     >  1:1008958/1‑149 (MQ=255)                                                                                                                aGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTaa                              <  1:3425/149‑1 (MQ=255)                                                                                                                  tgtttGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACt                            <  2:918269/147‑1 (MQ=255)                                                                                                                     ttGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTc                         <  2:164665/149‑1 (MQ=255)                                                                                                                        ctgcATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTcaaa                      <  2:1212344/149‑1 (MQ=255)                                                                                                                                  tGAGCGAATATTAACTCTGTGCATATTATAGTTTAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGataa            <  2:1348751/149‑1 (MQ=255)                                                                                                                                     gCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATAc         <  2:1223466/149‑1 (MQ=255)                                                                                                                                      cGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATAcc        >  2:936595/1‑149 (MQ=255)                                                                                                                                            ttAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATACcactaac  >  1:318647/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                              TGATTAATTCATCAGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCT‑AGAGGGCA‑TCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCCGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATACCACTCAC  >  NC_000913_3_pae_tpiA/1197358‑1197643

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑