Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,554,121	A→C	N169T (AAC→ACC)	BW25113_RS12740 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,554,121	0	A	C	100.0%	190.8 / NA	54	N169T (AAC→ACC)	BW25113_RS12740	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (35/19);  total (35/19)

CTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCA  >  NZ_CP009273/2554035‑2554203                                                                                       |                                                                                   cTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAccac                                                                                 <  1:500308/90‑1 (MQ=255)     gCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCATGCTATCAAAAACCACTGtt                                                                             >  1:150572/1‑90 (MQ=255)     gCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGtt                                                                             >  2:333929/1‑90 (MQ=255)                               gggATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCaa                                                   >  2:616830/1‑90 (MQ=255)                                      tGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTc                                            >  1:998944/1‑90 (MQ=255)                                        cAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCaa                                          <  1:541552/90‑1 (MQ=255)                                          gggTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCATGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAAc                                        >  1:129465/1‑90 (MQ=255)                                               ggTAGGGGAACAATCGACAAACGAGCCAGGCTGTCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCaa                                          >  2:379137/1‑83 (MQ=255)                                               ggTAGGGGAACAATCGACAAACGAGCCAGGCTGTCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCaa                                          <  1:379137/83‑1 (MQ=255)                                               ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCt                                                         <  2:134223/68‑1 (MQ=255)                                               ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCt                                                         >  1:134223/1‑68 (MQ=255)                                               ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt                                   >  1:489430/1‑90 (MQ=255)                                               ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt                                   >  1:95477/1‑90 (MQ=255)                                               ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt                                   >  1:155528/1‑90 (MQ=255)                                               ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt                                   >  1:820578/1‑90 (MQ=255)                                               ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt                                   >  1:188782/1‑90 (MQ=255)                                               ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt                                   >  1:482161/1‑90 (MQ=255)                                               ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt                                   >  2:440350/1‑90 (MQ=255)                                               ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt                                   >  1:60465/1‑90 (MQ=255)                                               ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt                                   >  2:705371/1‑90 (MQ=255)                                               ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt                                   >  1:372841/1‑90 (MQ=255)                                               ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt                                   >  2:631366/1‑90 (MQ=255)                                               gatAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt                                   >  2:66973/3‑90 (MQ=255)                                                  aGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAg                                <  2:630186/90‑1 (MQ=255)                                                    gggAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCg                              >  1:919817/1‑90 (MQ=255)                                                     ggAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGt                             >  2:201086/1‑90 (MQ=255)                                                      gAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTa                            >  2:603651/1‑90 (MQ=255)                                                      gAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTa                            >  1:812681/1‑90 (MQ=255)                                                      gAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTa                            >  2:218032/1‑90 (MQ=255)                                                      gAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTa                            >  1:497285/1‑90 (MQ=255)                                                      gAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTa                            >  1:924875/1‑90 (MQ=255)                                                      gAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTa                            >  1:950753/1‑90 (MQ=255)                                                       aaCAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTc                                                                 >  1:741095/1‑52 (MQ=255)                                                       aaCAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTc                                                                 <  2:741095/52‑1 (MQ=255)                                                         cAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTg                         >  1:881986/1‑90 (MQ=255)                                                         cAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTg                         >  1:818196/1‑90 (MQ=255)                                                          aaTCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGa                        >  2:113231/1‑90 (MQ=255)                                                           aTCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGaa                       >  2:944185/1‑90 (MQ=255)                                                            tCGACAAACGAGCCAGGCTATCAAAAACCATGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAg                      <  2:129465/90‑1 (MQ=255)                                                            tCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAg                      <  1:440350/90‑1 (MQ=255)                                                            tCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAg                      <  1:631366/90‑1 (MQ=255)                                                            tCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAg                      <  2:591783/90‑1 (MQ=255)                                                                cAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCta                  <  2:182297/90‑1 (MQ=255)                                                                cAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCta                  <  1:241289/90‑1 (MQ=255)                                                                cAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCta                  <  1:496093/90‑1 (MQ=255)                                                                 aaaCGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCtat                 <  1:81233/90‑1 (MQ=255)                                                                     gAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATAc             <  1:66973/90‑1 (MQ=255)                                                                      aGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATAcc            >  1:515521/1‑90 (MQ=255)                                                                             cTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCg     <  2:543632/90‑1 (MQ=255)                                                                             cTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCg     <  2:489430/90‑1 (MQ=255)                                                                             cTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCg     <  1:576380/90‑1 (MQ=255)                                                                             cTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCg     <  1:705371/90‑1 (MQ=255)                                                                                tCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAAcc                                                 >  1:207766/1‑43 (MQ=255)                                                                                tCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAAcc                                                 <  2:207766/43‑1 (MQ=255)                                                                                tCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCa  >  2:234485/1‑90 (MQ=255)                                                                                       |                                                                                   CTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCA  >  NZ_CP009273/2554035‑2554203

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑