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%	105.6 / NA	34	G11R (GGA→AGA)	ymfD	e14 prophage; putative SAM‑dependent methyltransferase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (21/13);  total (21/13)

TGATTAATTCATCAGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCCGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATACCACTC  >  NC_000913_3_pae_tpiA/1197358‑1197641                                                                                                                                                 |                                                                                                                                            tGATTAATTCATCAGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGc                                                                                                                                         >  1:469183/1‑149 (MQ=255)               gAATATATAAGTTTTCAGCCTCTGGAGTAAAGGGCGAGGCCATTTTTCTCAATGCTTCTAATATATACGCAAAGATATCTAGAGGCGCTCGTATTAGGATTTGAGTCATTCGCTGATCGACTCTTATTAGTGTGAATATTATAGTTCaa                                                                                                                           >  2:695555/1‑149 (MQ=255)                aaTATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCaaa                                                                                                                          <  1:187949/149‑1 (MQ=255)                            ttCCTCAGACAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTTTAATATACTCGCAAAAATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCAtt                                                                                                              <  2:321533/149‑1 (MQ=255)                                 cAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAAtt                                                                                                         >  2:51059/1‑149 (MQ=255)                                   gCCAAAATCAAGGGGGTGGCCATTTTTCTCAATGGGTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTaa                                                                                                       <  2:741852/149‑1 (MQ=255)                                        aaTCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCCTGCAAGCAATGTTa                                                                                                  >  2:88578/1‑149 (MQ=255)                                             aGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTAttttt                                                                                             >  2:765384/1‑149 (MQ=255)                                              gggCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTa                                                                                            <  2:194364/149‑1 (MQ=255)                                                   tGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGaa                                                                                       >  1:817429/1‑149 (MQ=255)                                                         tttttCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTc                                                                                 >  1:591725/1‑149 (MQ=255)                                                              ctcAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCtttta                                                                            >  1:833050/1‑149 (MQ=255)                                                               tcAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTTttttat                                                                           >  2:128346/1‑149 (MQ=255)                                                                    gCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTtttattttat                                                                      >  1:357106/1‑149 (MQ=255)                                                                    gCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTtttattttat                                                                      <  2:616054/149‑1 (MQ=255)                                                                     cTTCTAATATACTCGCAAAGATATATAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATc                                                                     <  2:666376/149‑1 (MQ=255)                                                                        cTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTCAAAAATTCTTTTATTTTATCGTc                                                                  >  2:808684/1‑149 (MQ=255)                                                                                cTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGAttt                                                          >  1:171611/1‑149 (MQ=255)                                                                                 tCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGAtttt                                                         >  1:251484/1‑149 (MQ=255)                                                                                      aaGATATCTAGAGGGCAGCGTAAGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTACAAAGCAAGTACCATTCAATTAATGTTAAAAAAAAAAAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCga                                                    <  2:588151/149‑1 (MQ=255)                                                                                       aGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCgac                                                   <  2:352219/149‑1 (MQ=255)                                                                                         atatCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCgactt                                                 <  1:765384/149‑1 (MQ=255)                                                                                             cTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAATTACCATTTAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCgacttgact                                             <  2:829899/149‑1 (MQ=255)                                                                                                   ggCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGt                                       >  1:850985/1‑149 (MQ=255)                                                                                                   ggCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGt                                       >  1:18651/1‑149 (MQ=255)                                                                                                     cATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCGGttt                                     >  1:78526/1‑148 (MQ=255)                                                                                                                      ctgcATTCGCTAGGCGAATATTAACTCTGTGCATATTCTCGTTCCCCGCTCGTCTCAATCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTcaaa                    <  2:817429/149‑1 (MQ=255)                                                                                                                         cATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCGCAACTTGGCTTAACTGTcaaagca                 >  2:851402/1‑149 (MQ=255)                                                                                                                              tctGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGGCTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGat            >  1:66618/1‑149 (MQ=255)                                                                                                                              tctGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCACTCAATTCATGTTATTTTAAGTAGATATTTATTTTTTCTTATCGTCCTTTATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGat            >  1:382509/1‑149 (MQ=255)                                                                                                                               ctGAGCCAATATTAACTCTTGGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGata           <  1:88578/149‑1 (MQ=255)                                                                                                                                   gggAATATTAACTTTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATAc       <  1:274272/147‑1 (MQ=255)                                                                                                                                      aaTATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTACGACTTCACTTTCCATTCTCGGCTTAACTGTCAAAGCAAAAATAATACcac    >  2:708063/1‑149 (MQ=255)                                                                                                                                        tatTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCGAAGATAATACcactc  >  2:795736/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                            TGATTAATTCATCAGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCCGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATACCACTC  >  NC_000913_3_pae_tpiA/1197358‑1197641

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑