Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,593,447	T→C	S52P (TCC→CCC)	yjjQ →	response regulator transcription factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,593,447	0	T	C	100.0%	65.8 / NA	20	S52P (TCC→CCC)	yjjQ	response regulator transcription factor
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (11/9);  total (11/9)

GGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACAA  >  NZ_CP009273/4593365‑4593530                                                                                   |                                                                                    ggTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAtt                                                                              >  2:342901/1‑90 (MQ=255)  gTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTa                                                                             <  2:5196/90‑1 (MQ=255)     aTGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTc                                                                          <  2:324480/90‑1 (MQ=255)     aTGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTc                                                                          <  2:314998/90‑1 (MQ=255)          gACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGc                                                                     <  1:345708/90‑1 (MQ=255)                            tGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAg                                                   >  2:15743/1‑90 (MQ=255)                                        cAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACg                                       >  1:151507/1‑90 (MQ=255)                                          gcgcCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCAc                                        <  1:318396/87‑1 (MQ=255)                                          gcgcCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCAc                                        >  2:318396/1‑87 (MQ=255)                                            gcCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCt                                   >  1:88269/1‑90 (MQ=255)                                              ctctGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGt                                 >  1:393602/1‑90 (MQ=255)                                                  gCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTtgt                             >  1:427178/1‑90 (MQ=255)                                                      aggaCCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAAc                         <  1:374975/90‑1 (MQ=255)                                                      aggaCCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAAc                         <  2:393602/90‑1 (MQ=255)                                                         accttaccttATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACat                       <  2:268901/89‑1 (MQ=255)                                                         accttaccttATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACat                       >  1:268901/1‑89 (MQ=255)                                                          ccttaccttaTTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACatta                     >  1:267400/1‑90 (MQ=255)                                                            ttaccttaTTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACattatt                   >  2:260253/1‑90 (MQ=255)                                                                            aCGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTcaca   >  1:111707/1‑90 (MQ=255)                                                                             cgtcgtCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACaa  <  1:475325/90‑1 (MQ=255)                                                                                   |                                                                                    GGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACAA  >  NZ_CP009273/4593365‑4593530

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑