Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,823,162	C→T	H255Y (CAC→TAC)	spoT →	bifunctional (p)ppGpp synthase/hydrolase SpoT

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,823,162	0	C	T	100.0%	60.5 / NA	22	H255Y (CAC→TAC)	spoT	bifunctional (p)ppGpp synthase/hydrolase SpoT
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (9/13);  total (9/13)

CGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGATCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTCACTCGATCATGGACATCTACGCTTTCCGCGTGATCGTCAATGATTCTGACACCTGTTATCGCGTGCTGGGCCAGATGCACAGCCTGTACAAGCCGCGTCCGGGCCGCGTGAAAGACTATATCGCCATTCCAAAAGCGAACGGCTATCAGTCTTTGCACACCTCGATGATCGGCCCGCACGGTGTGCCGGTTGAGGTCCAGATCCGTACCGAAGATATGGACCAGATGGCGGAGATGGGTGTTGC  >  NC_000913/3822939‑3823406                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                     cGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCTTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGATCCAGAAGATTTTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGGGGTCGCTAGAAGCATCTTTATTCGATTTACGGCAAAATGGTGCTCAAAGAGCAGCGTTTTTACTCGATCATGGACATCTACGCTTTcc                                                                                                                                                                                                                           <  1:260115/251‑1 (MQ=255)                                                              gtggtgAAAGCCGCGCGCGGCAACCGTAAAGAGATGATCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTTACTCGATCATGGACATCTACGCTTTCCGCGTGATCGTCAATGATTCTGACACCTGTTa                                                                                                                                                                                            >  1:309294/1‑221 (MQ=255)                                                              gtggtgAAAGCCGCGCGCGGCAACCGTAAAGAGATGATCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTTACTCGATCATGGACATCTACGCTTTCCGCGTGATCGCCAATGATTCTGACACCTGTTa                                                                                                                                                                                            >  1:309323/1‑221 (MQ=255)                                                                         cgcgcgcgGCAACCGTAAAGAGATGATCCAGAATATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGGGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACGGCAAAATGGTGGTCAAAGAGCAGCGTTGTTACTCGATCATGGACAGCTCCGCTTTTCGCGTGATCGTTAGTGATTCTGACACCTGTTATCGCGTGCTGGGCCAGATGCACAGCCTGTACAAGCCGCGTc                                                                                                                                                   <  1:327179/251‑1 (MQ=255)                                                                          gcgcgctGCAACCGTAAAGAGATGATCCAGAAGATTCTTTCTGAAATCGAAGCGAGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTTACTCGATCATGGACATCTACGCTTTCCGCGTGATCGTCAATGATTCTGACACCTGTTATCGCGTGCTGGGCCAg                                                                                                                                                                            >  1:65179/1‑225 (MQ=255)                                                                               cgGCAACCGTAAAGAGATGATCCAGAAGATTCTTTCTGAAATCGAAGGGCGATTGCAGGCAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTTACTCGATCATGGACATCTACGCTTTCCGCGTGATCGTCAATGATTCTGACACCTGTTATCGCGTGCTGGGCCAGATGCACAGCCTGTACAAGCCGCGTCCGGGcc                                                                                                                                             >  1:303196/1‑251 (MQ=255)                                                                                 gCAACCGTAAAGAGATGATCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTTACTCGATCATGGACATCGACGCTTTCCTCGTGATCGTCAATGATTCTGACAcc                                                                                                                                                                                                 <  1:351321/197‑1 (MQ=255)                                                                                                    ccAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTTACTCGATCATGGACATCTACGCTTTCCGCGTGATCGTCAATGATTCTGACACCTGTTATCGCGTGCTGGGCCAGATGCACAGCCTGTACAAGCCGCGTCCGGGCCGCGTGAAAGACTATATCGcc                                                                                                                         >  1:361237/1‑250 (MQ=255)                                                                                                     cAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTTACTCGATCATGGACATCTACGCTTTCCGCGTGATCGTCAATGATTCTGACAcc                                                                                                                                                                                                 >  1:231056/1‑177 (MQ=255)                                                                                                           aTTCTGTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTTACGCTATCATGGACATCTACGCTTGCCGCGTGATCGTCAATGAGTCTGACACCTGTTATcgcn                                                                                                                                                                                       <  1:78586/181‑2 (MQ=255)                                                                                                                                   ttGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTTACTCGATCATGGACATCTACGCTTTCCGCGTGATCGTTAATGATTCTGACGCCTGTTAGCGCGTGCTGGGCCAGATGCACAGTCTTTACAAGCCGCGTCCGGGCCGCGTGAAAGACTATATCGCCATTCCAAAAGCGAACGGCTATCAGTCTTTGc                                                                                          <  1:330493/250‑1 (MQ=255)                                                                                                                                   tnNCAGGAANNGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTTACTCg                                                                                                                                                                                                                                                 <  2:31111/99‑1 (MQ=255)                                                                                                                                         gAAGCGTGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTTACTCGATCATGGACATCTACGCTTTCCGCGTGATCGTCAATGATTCTGACACCTGTTATCTCGTGCTGGGCCAGATGCACAGCCTGTACAAGCCGCGTCCGGGCCGCGTGAAAGACtat                                                                                                                               <  1:198804/207‑1 (MQ=255)                                                                                                                                                             cggcAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGTGTTTTTACTCGAGCATGGACATCTTCGCTTTCCGCGTGATCGTCAATGATTCTGACACCTGTTATCGCGTGCTGGGc                                                                                                                                                                               <  1:202346/136‑1 (MQ=255)                                                                                                                                                                                    tttATNCGATTNANNGCAAAATGGTGCTCAAAGANCAGCGTTTTTACTCGNTCATNGACATNTANg                                                                                                                                                                                                                                 >  2:186471/1‑66 (MQ=255)                                                                                                                                                                                                    cAAAATGGTGCTCAAAGAGCAGTGTTTTTACTCGATCATGGACATCTACGCTTTCCGCGTGATCGTCAATGATTCTGACACCTGTTATCGCGTGCTGGGCCAGATGCACAGCCTGTan                                                                                                                                                             <  1:48733/118‑2 (MQ=255)                                                                                                                                                                                                              cTCAAAGATCAGCGTTTTTACGCGATCATGGACATCTACGCTTTCCGCGTGATCGTCAATGATTGTGACACCTGTTATCGCGTGCTGGGCCAGATGCACAGCCTGTACAGGCCGCGt                                                                                                                                                    <  1:67090/117‑1 (MQ=255)                                                                                                                                                                                                              cTCAAAGAGCAGCGTTTTTACTCGATCATGGACATCTACGCTTTCCGCGTGATCGTCAATGATTCTGACACCTGTTATCGCGTGCTGGNNCAGATGnnc                                                                                                                                                                      >  2:15727/1‑99 (MQ=255)                                                                                                                                                                                                              cTCAAAGAGCAGCGTTTTTACTCGATCATGGACATCTACGCTTTCCGCGTGATCGTCAATGATTCTGACACCGGTTATCGCGTGCTGGGCCAGATGCACAGCCTGTACAAGCCGCGTCCGGGCCGCGTGAAAGACTATATCGCCAt                                                                                                                       <  1:15727/146‑1 (MQ=255)                                                                                                                                                                                                                cAAAGAGCAGCGTTTTTACTCGATCATGGACATCTACGCTTTCCGCGTGATCGTCAATGATTCTGACACCTGTTATCGCGTGCTGGGCCAGATGCACAGCCTGTACAAGCCGCGTCAGGGCCGCGTGACAGACTATATCGACATTCCAAAAGCGAACGGCTATCAGTCTTTGCACACCTCGCTGATCGGCCCGAACGGTGTGCCGGTTGAGGTCCAGATCCGTACCGAAGATATGGACCAGATGGCgg               >  1:231803/1‑248 (MQ=255)                                                                                                                                                                                                                          cGTTTTTACTCGATCATGGACATCTACGCTTTCCGCGTGATCGTCAATGATTCTGACACCTGTTATCGCGTGCTGGGCCAGATGCACAGCCTGTACAAGCCGCGTCCGGGCCGCGTGAAAGACTATATCGCCATTCCAAAAGCGAACGGCTATCAGTCTTTGCACACCTCGATGATCGGCCCGCACGGTGTGCCGGTTGAGGTCCAGATCCGTACCGAAGATATGGACCAGATGGCGGAGATGGTTGTTGc  <  1:120212/251‑1 (MQ=255)                                                                                                                                                                                                                            ttttTACTCGATCATGGACATCTACGCTTTCCGCGTGATCGGCAATGATTCTGACACCTGTTATCGCGTGCTGGGCCAGATGCACAGCCTGTACAAGCCGCGTCCGGGCCGCGTGAAAGACTATATCGCCATTCCAAAAGCGAACGGCTATCAGTCTTTg                                                                                           <  1:415486/160‑1 (MQ=255)                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                     CGAACTCGAAGAGCTGGGTTTTGAGGCGCTGTATCCCAACCGTTATCGCGTAATCAAAGAAGTGGTGAAAGCCGCGCGCGGCAACCGTAAAGAGATGATCCAGAAGATTCTTTCTGAAATCGAAGGGCGTTTGCAGGAAGCGGGAATACCGTGCCGCGTCAGTGGTCGCGAGAAGCATCTTTATTCGATTTACTGCAAAATGGTGCTCAAAGAGCAGCGTTTTCACTCGATCATGGACATCTACGCTTTCCGCGTGATCGTCAATGATTCTGACACCTGTTATCGCGTGCTGGGCCAGATGCACAGCCTGTACAAGCCGCGTCCGGGCCGCGTGAAAGACTATATCGCCATTCCAAAAGCGAACGGCTATCAGTCTTTGCACACCTCGATGATCGGCCCGCACGGTGTGCCGGTTGAGGTCCAGATCCGTACCGAAGATATGGACCAGATGGCGGAGATGGGTGTTGC  >  NC_000913/3822939‑3823406

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑