Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,553,272	C→T	S63L (TCG→TTG)	malT →	DNA‑binding transcriptional activator MalT

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,553,272	0	C	T	100.0%	65.1 / NA	25	S63L (TCG→TTG)	malT	DNA‑binding transcriptional activator MalT
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (13/12);  total (13/12)

TTTCCACAGTGAAGTGATTAACTATGCTGATTCCGTCAAAACTAAGTCGTCCGGTTCGACTCGACCATACCGTGGTTCGTGAGCGCCTGCTGGCTAAACTTTCCGGCGCGAACAACTTCCGGCTGGCGCTGATCACGAGTCCTGCGGGCTACGGAAAGACCACCCTCATTTCCCAGTGGGCGGCAGGCAAAAACGATATCGGCTGGTACTCGCTGGATGAAGGTGATAACCAGCAAGAGCGTTTCGCCAGCTATCTCATTGCCGCCGTGCAGCAGGCAACCAACGGTCACTGTGCGATATGTGAGACGATGGCGCAAAAACGGCAATATGCCAGCCTGACGTC  >  NC_000913/3553062‑3553404                                                                                                                                                                                                                   |                                                                                                                                     tttCCACAGTGAAGTGATTAACTATGCTGAGTCCGTCAAAACGAAGTCGTCCGGTTCGACTCGACCATACCGTGGTTCGTGAGCGCCTGCTGGCTAAACTTGCCGGCGCGAACAACTTCCGGCTGGCGCTGATCTCGAGTCCTGCGGGCTACGGAAAGACCACCCTCATTTCCCAGTGGGCGGCAGTCAAAAACGATATCGGCTGGTACTTGCTGGATGAAGGTGATAACCAGCAAGAGCGTTTCTCCat                                                                                               <  1:297161/250‑2 (MQ=255)       caGTGAAGTTATTAACGATGCTGATTCCGTCAAAACCAAGTCGTCCGGTTCGACTCGACCATACCGTGGTTCGTGAGCGCCTGCTGGCTAAACTTTCCGGCGCGAACAACTTCCTGCTGGCGCTGATCACCAGTCCTGCGGGCTACGGAAAGACCACCCTCATTTCCCAGTGGGCGGCAGTCAAAAACGATATCGGCTGGTACTTGCTGGATGAAGGTGATAACCAGCAAGAGCGTTTCGCCAGCTAtctc                                                                                        <  1:86058/251‑1 (MQ=255)       caGTGAAGTGATTAACTATGCTGATTCCGTCAAAACTAAGTCGTCCGGTTCGACTCGACCATACCGTGGTTCGTGAGCGCCTGCTGGCTAAACTTTCCGGCGCGAACAACTTCCGGCTGGCGCTGATCACGAGTCCTGCGGGCTACGGAAAGACCACCCTCATTTCCCAGTGGGCGGCAGGCAAAAACGATATCGGCTGGTACTTGCTGGATGAAGGTGATAACCAGCAAGAGCGTTTCGCCAGCTAtctc                                                                                        <  1:86067/251‑1 (MQ=255)                                   gTCAAAACTAAGTCGTCCGGTTCGACTCGACCATACCGTGGTTCGTGAGCGCCTGCTGGCTAAACTTTCCGGCGCGACCAACTTCCGGCTGGCGCTGATCACGAGTCCTGCGGGCTACGGAAAGACCACCCTCATTTCCCAGTGGGCGGCAGGCAAAAACGTTATCGGCTGGTACTTGCTGGATGAAGGTGATAACCAGCAAGAGCGTTTCGCCAGCTATCTCATTGCCGCCGTGCAGCAGGc                                                                    >  1:155952/1‑243 (MQ=255)                                                     ggTTCGACTCGACCATACCGTGGTTCGTGAGCGCCTGCTGGCTAAACTTTCCGGCGCGAACAACTTCCGGCTGGCGCTGATCACGAGTCCTGCGGGCTACGGAAAGACCACCCTCATTTCCCAGTGGGCGGCAGGCAAAAACGATATCGGCTGGTACTTGCTGGATGAAGGTGATAACCAGCAAGAGCGTTTCGCCAGCTATCTCATTGCCGCCGTGCAGCAGGCAACCAACGGTCACTGTGCGATAtgtn                                          <  1:131570/251‑2 (MQ=255)                                                              cgacCATACCGTGGTTCGTGAGAGCCTGCTGGCTAAACTTTCCGGCGCGAACAACTTCCGGCTGGCGCTGATCACGAGTCCTGCGGGCTACGGAAAGACCACCCTCATTTCCCAGTGGGCGGCAGGCAAAAACGATATCGGCTGGTACTTGCTGGATGAAGGTGATAACCAGCAAGAGCGTTTCGCCAGCTATCTCATTGCCGCCATGCAGCAGGCAACCAACGGTCACTGTGCGATATGTGAGACGATgg                                 >  1:111694/1‑251 (MQ=255)                                                                        ntGGTTCGTGAGCGCCTGCTGGCTAAACTTTCCGGAGAGCAAAACTTCCAGCTGGCGCTGATCACGAGTCCTGCGGGCTACGGAAAGACCACCCTCATTTCCCAGTGGGCGGCCGGCCAAAACGATATCGGCTGGTACTTGCTGGGTGAAGGTGATAACCAGCAAGAGCGTTTCGCCAGCTATCTCATTgccgc                                                                                >  1:101573/2‑194 (MQ=255)                                                                           gTTCGTGAGCGCCTGCTGGCTAAACTTTCCGGCGCGAACAACTTCCGGCTGGCGCTGATCACGAGACCTGCGGGCTACGGAAAGACCACCCTCATTTCCCAGTGGGCGGCAGGCAAAAACGATATCGGCTGGTACTTGCTGGATGAAGGAGATAACCAGCAAGAGAGTTTCGCCAGCTATCTCATTGCCGCAGTGCAGCAGGCAACCAACGGTCACTGTGCGatat                                             >  1:279928/1‑226 (MQ=255)                                                                           gTTCGTGAGCGCCTGCTGGCTAAACTTTCCGGCGAGTACAACGTCCGGCTGGCGCTGATCACGAGTCCTGCGGGCTACGGAAAGACCACCCTCATTTCCCAGTGGGCGGCTGGCAAAAACGATATCGGCTGGTACTTGCTGGATGAAgg                                                                                                                          <  1:363439/149‑1 (MQ=255)                                                                                              cTAAACTTTCCGGCGCGAACAACTTCCGGCTGGCGCTGCTCACGAGTCCTGCAGGCTATGGAAAGAGCACCCTCATTTCACAGTGGGCGGCAGGCCAAAACGATATCGGCTGGTCCTTGCTGGATGAAGGTGATAACCAGCAAGGGCGTTTCGCCAGCTATCTCATTGCCGCGGTGCAGCAGGCAACCAACGGTAAATGTGCGATATGTGTGCCGTTGGGGCAAAAACggacatctgcccgcccgatcgg  >  1:86577/1‑230 (MQ=255)                                                                                              cTAAACTTTCCGGCGCGAACAACTTCCGGCTGGCGCTGATCACGCGTCCTGAGGGCAACGGAAAGTCCACCATATTTTCCCCGGGGGAGACAAGCAAAAACGATATCGGCTGGAACTTGCTGGCTGAAGGCGATAACCAGCAACCGCGTTTCGCCAGCTATCTCATTGCCGCAGTGCAGCCGGCAACCAACGAACACTGAGCGATATGTTAGACGATg                                  >  1:330720/1‑218 (MQ=255)                                                                                                         ggCGCGAACAACTTCCGGCTGGCGCTGATTACGAGTCCTGCGGGCTACGGAAAGACCACCCTCCTTTCCCAGTGGGCGGCAGGCAAAAACGATATCGGCTGGTACTTGCTGGATGAAGGTGATAACCAGCAAGAGCGTTTCGCCAGCTCTCTCATTGCCGCCGTGCAGCAGGCAACCAACGGTCACTGTGCGATATGTGAGACGATGGCGCAAAAACGGCAat                  >  1:69866/1‑223 (MQ=255)                                                                                                         ggCGCGAACAACTTCCGGCTGGCGCTGATCACGAGTCCCGCCGGCTACGGAAAGACCACCCTCATTTCCCAGTGGGCGGCAGGCAAAAACGATATCGGCTGGGACTTGCTGGATGAAGGTGATAACCAGCAAGAGCGTTTCGCCAGCTATCTCATTGCAGCCGGGCAGCAGGcaac                                                                 >  1:449584/1‑176 (MQ=255)                                                                                                              gAACAACTTCCGGCTGGCGCTGATCACGAGTCCTGCGGGCTACGGAAAGACCACCCTCATTTCCCAGTGGGCGGCAGGCAAAAACGATATCGGCTGGTACTTGCTGGATGAAGGTGATAACCAGCAAGAGCGTTTCg                                                                                                   >  1:13222/1‑137 (MQ=255)                                                                                                                acaacTTCCGGCTGGCGCTGATCACGAGTCCTGCGGGCTACGGAAAGACCCCCCTCATTTCCCAGTGGGCGGCAGGCAAAAACGATATCGGCTGGTACTTGCTGGATGAAGGTGATAACCAGCAAGAGCGTTGCGCCAGCTATCTCATTGCCGCCGTGCAGCAGGCAACCAACGGTc                                                         <  1:391687/177‑1 (MQ=255)                                                                                                                                   gATCACGAGTCCTGCGGGCTACGGAAAGACCACCCTCATTTCCCAGTGGGCGGCAGGCAAAAACGATATCGGCTGGTACTTGCTGGATGAAGGTGATAACCAGCAAGAGCGTTTCGCCAGCTATCTCATTgccgn                                                                                <  1:61638/135‑2 (MQ=255)                                                                                                                                    aTCACGAGTCCTGCGGGCTACGGAAAGACCACCCTCATTTCCCAGTGGGCGGCAGGCAAAAACGATCTCGGCTGGTACTTGCTGGATGAAGGTGATAACCAGCAAGAGCGTTTCGCCAGCTATCTCATTGCCGCCGTGCAGCAGGCAACCAACGGTCACTGTGCGATATGTGAGACGATGGCGCAAAAACg                       >  1:212877/1‑191 (MQ=255)                                                                                                                                             ccTGCGGGCTACGGAAAGACCACCCTCATTTCCCAGTGGGCGGCAGGCAAAAACGATATCGGCTGGTACTTGCTGGATGAAGGTGATAACCAGCAAGAGCGTTTCGCCAGCTATCTCATTGCCGCCGTgc                                                                           <  1:286113/130‑1 (MQ=255)                                                                                                                                                gNGGGNTNNGNNAAGNCCACCCTCATTTCCCAGTGGGNNGCAGGCAAANACGATATCGGCTGGTACTTGCTGGATGAAGGTGATAACCAGCAAGAGCGTTTCNCCAGCTATCNNATNGCCGCNANNNANNNGGNAACCAACGGTCACTGTGCGNTANNTGAGACNATGGCGCAAAAACGGCAATATGCCAg           <  2:111694/191‑1 (MQ=255)                                                                                                                                                        cGGAAAGACCACCCTCATTTCCCAGTGGGCGGCAGGCAAAAACGATAGCGGCTGGTACTTGCTGGATGAAGGTGATAACCAGCAAGAGcn                                                                                                        <  1:130282/90‑2 (MQ=255)                                                                                                                                                                                      tgcaggcaAAAACGATATCGGCTGTTACTTGCTGGATGAAGGTGATAACCAGCAAGAGCGTTTCGGCATCTATCTCATTGCCGCCGTGCAGCAGGCAACCAACGGTCACTGTGCGATATGTGAGACGATGgccc                              <  1:480391/133‑3 (MQ=255)                                                                                                                                                                                            caAAAACGATATCGGCTGGTACTTGCTGGATGAAGGTGATCACCAGCAAGAGCGTTTCGCCAGCTATCTCATTGCCGCCGTGCAGCAGGCAACCAACGGTCACTGTGCGATATGTGAGACGATGGCGCAAAAACGGCAATATGACAGCCTGACGTc  >  1:297022/1‑156 (MQ=255)                                                                                                                                                                                               aaaCGATATCGGCTGGTACTTGCTGGATGAAGGGGATAACCAGCAAGAGCGATTCGCCAGCTATCTCATTGCCGCCGTGCAGCAGGCAACCAACGGTCACTGTGCGATATGTGAGACGATGgcgc                              >  1:448355/1‑125 (MQ=255)                                                                                                                                                                                                              gTACTTGCTGGATGAAGGTGATAACCAGCAAGAGCGTTTCGCCAGCTATCTCATTGCCGCCGTgc                                                                           <  1:33027/65‑1 (MQ=255)                                                                                                                                                                                                              gTACTTGCTGGATGAAGGTGATAACCAGCAAGAGCGTTTCGCCAGCTATCTCATTGCCGCCGTgc                                                                           >  2:33027/1‑65 (MQ=255)                                                                                                                                                                                                                   |                                                                                                                                     TTTCCACAGTGAAGTGATTAACTATGCTGATTCCGTCAAAACTAAGTCGTCCGGTTCGACTCGACCATACCGTGGTTCGTGAGCGCCTGCTGGCTAAACTTTCCGGCGCGAACAACTTCCGGCTGGCGCTGATCACGAGTCCTGCGGGCTACGGAAAGACCACCCTCATTTCCCAGTGGGCGGCAGGCAAAAACGATATCGGCTGGTACTCGCTGGATGAAGGTGATAACCAGCAAGAGCGTTTCGCCAGCTATCTCATTGCCGCCGTGCAGCAGGCAACCAACGGTCACTGTGCGATATGTGAGACGATGGCGCAAAAACGGCAATATGCCAGCCTGACGTC  >  NC_000913/3553062‑3553404

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑