Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_vch_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_vch_tpiA	1,197,502	0	C	T	100.0%	154.7 / NA	48	G11R (GGA→AGA)	ymfD	e14 prophage; putative SAM‑dependent methyltransferase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (25/23);  total (25/23)

TGATTAATTCATCAGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCCGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATACCACTCAC  >  NC_000913_3_vch_tpiA/1197358‑1197643                                                                                                                                                 |                                                                                                                                              tGATTAATTCATCAGAATATCTAAGTTTTCCGCAGCCAAAATCAAAGGCGTGGTGATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGc                                                                                                                                           >  1:586230/1‑149 (MQ=255)  gATTAATTCATCAGAATATCTAAGTTTGCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCa                                                                                                                                          <  2:591736/149‑1 (MQ=255)        ttCATCAGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCAtattat                                                                                                                                    >  2:568640/1‑149 (MQ=255)            tcaGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGtt                                                                                                                                <  1:801805/149‑1 (MQ=255)               gAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCACAAAGATATCTAGAGGGCATCGTATGAAGTATTGCTGCATTCTCTGAACGAATATTAACTCTGTGCATTTTATAGTTaaa                                                                                                                             >  1:718334/1‑149 (MQ=255)                      tAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGt                                                                                                                      >  2:202381/1‑149 (MQ=255)                            ttCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCAtt                                                                                                                <  1:658166/149‑1 (MQ=255)                                            aaGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGAATGAGGTTTTGCTGCATTCTATGAGCGAATATTAGCTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCACTCAATGTTAtttt                                                                                                >  2:664106/1‑149 (MQ=255)                                                gCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGt                                                                                            <  1:568640/149‑1 (MQ=255)                                                    ggCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTTCCATTCATTTAATGTTATTTTTTCTGaaa                                                                                        >  2:189824/1‑149 (MQ=255)                                                    ggCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGaaa                                                                                        >  1:493264/1‑149 (MQ=255)                                                         tttttCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTCCCCTTCAATTAATGTTATTTTTAGTGAAAAATTc                                                                                   <  2:394935/149‑1 (MQ=255)                                                         tttttCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTc                                                                                   >  2:567140/1‑149 (MQ=255)                                                         tttttCTCAATGCTTCTAATATACTCGCAAAGATATCTAGACGGCACCCTATGACGTTCCCCTGCAACCTCTCAACCAAGACTAAGTCTGTGCAAGTTATAGTTCAAAGCAAGCACCATCCAATTAATGTTACTTTTCGTGaaaaacta                                                                                   >  2:92663/1‑146 (MQ=255)                                                                 aaTGCTTCTAATAAAATCGCAAAGATATCTAGAGGGCATCGTATGCGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGGATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGGAAAATTCttttattt                                                                           >  2:406577/1‑149 (MQ=255)                                                                          aaTATACTCGCAAAGATATGTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCg                                                                  <  1:500083/149‑1 (MQ=255)                                                                           atatACTCGCAAAGATATCTAGAGGGCATCGAATGAGGTTTTGCTTCATTCTCTTAGCGAATATTAACTCTTTTCTTATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTcccg                                                                 >  2:704624/1‑147 (MQ=255)                                                                                   gCAAAGGTATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTc                                                         <  1:384892/149‑1 (MQ=255)                                                                                   gCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTGTAGTGAAAAATTCTTTTTTTTTATCGTTCGGGATTTTTc                                                         >  2:462831/1‑149 (MQ=255)                                                                                      aaGATATGTAGAGGGGATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCga                                                      <  2:648797/149‑1 (MQ=255)                                                                                      aaGATAGCTAGAGGGTATCTTATGAGTTTTTGCTGCATTCTCTGCGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCga                                                      <  1:261496/149‑1 (MQ=255)                                                                                              tAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCgacttgactt                                              >  1:660097/1‑149 (MQ=255)                                                                                                  gggCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTA‑TTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGt                                         >  1:183679/1‑149 (MQ=255)                                                                                                     cATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTc                                       <  1:567140/149‑1 (MQ=255)                                                                                                         gtttGAGGTTTTGCTGCATTCTCTGAGGCAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTggg                                   <  1:743758/146‑1 (MQ=255)                                                                                                         gTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTggg                                   <  1:566326/149‑1 (MQ=255)                                                                                                         gTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTggg                                   <  1:541500/149‑1 (MQ=255)                                                                                                          tATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACttt                                             >  2:722297/1‑138 (MQ=255)                                                                                                          tATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACttt                                             <  1:722297/138‑1 (MQ=255)                                                                                                          tATGAGGGTTTGCTGCATTCTCTGAGCGACTAGTAACACTGTGCAGATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGc                                  <  2:677040/149‑1 (MQ=255)                                                                                                              aGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACttt                                             <  1:144765/134‑1 (MQ=255)                                                                                                              aGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACttt                                             >  2:144765/1‑134 (MQ=255)                                                                                                              aGGTTTTGCTGCATTCTCTGAGCGAATATTAACGCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTaa                              <  1:132791/149‑1 (MQ=255)                                                                                                               ggTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAAc                             <  2:660097/149‑1 (MQ=255)                                                                                                                gTTTTGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACt                            >  2:790916/1‑149 (MQ=255)                                                                                                                  tttGCTGCATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGt                          <  2:271710/149‑1 (MQ=255)                                                                                                                     gctgcATTCTCTGAGCGAATATTAACTCTCTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATTTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTcaa                       <  1:722342/149‑1 (MQ=255)                                                                                                                        gcATTCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTcaaagc                    >  1:814695/1‑149 (MQ=255)                                                                                                                           ttCTCTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTcaaagcaaa                 <  1:300531/149‑1 (MQ=255)                                                                                                                            tctcTGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTcaaagcaaag                >  1:751431/1‑149 (MQ=255)                                                                                                                                tGAGCGAATATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGataa            >  2:71213/1‑149 (MQ=255)                                                                                                                                  agtcaaTATTAACTATGTGCATATTATAGTTCAAAGCAAGTACCAATCAATTAATGTTATTTTTAGTGAAAAATTCTTTTACTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGataata          <  1:33364/145‑1 (MQ=255)                                                                                                                                      aaTATTAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATACcac      >  1:610368/1‑149 (MQ=255)                                                                                                                                        tatTAACTCTGTGCATGTTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTAAAAGCAAAGATAATACcactc    >  2:227642/1‑149 (MQ=255)                                                                                                                                          ttAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCttttatttt                                                                          <  1:737579/77‑1 (MQ=255)                                                                                                                                          ttAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCttttatttt                                                                          >  2:737579/1‑77 (MQ=255)                                                                                                                                          ttAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCCGTTCTGGGCTTAACTGTCAAAGCCAAGATAATACcactcac  >  1:72074/1‑149 (MQ=255)                                                                                                                                          ttAACTCTGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTGTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATACcactcac  >  1:797808/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                              TGATTAATTCATCAGAATATCTAAGTTTTCCGCAGCCAAAATCAAGGGCGTGGCCATTTTTCTCAATGCTTCTAATATACTCGCAAAGATATCTAGAGGGCATCGTATGAGGTTTTGCTGCATTCTCTGAGCGAATATTAACTCCGTGCATATTATAGTTCAAAGCAAGTACCATTCAATTAATGTTATTTTTAGTGAAAAATTCTTTTATTTTATCGTCCGGGATTTTTCCGACTTGACTTTCAGTTCTGGGCTTAACTGTCAAAGCAAAGATAATACCACTCAC  >  NC_000913_3_vch_tpiA/1197358‑1197643

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑