Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	281,662	Δ1 bp	coding (322/1155 nt)	yagA ←	CP4‑6 prophage, putative DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	281,660	0	G	.	100.0%	132.7 / NA	32	coding (324/1155 nt)	yagA	CP4‑6 prophage, putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (16/16);  total (16/16)

AAAGTGGCCCTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGACGGTCATGGGCCATACGCAGCAGGGCCGTGATGTCGTCAGATGAGCGGTTCGGGGAATGGTGCGG  >  NC_000913/281525‑281788                                                                                                                                        |                                                                                                                                 aaaGTGGCCCTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCggca                                                                                                                               <  1:417374/139‑3 (MQ=255) aaaGTGGCCCTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCggca                                                                                                                               <  2:47044/139‑3 (MQ=255)       gCCCTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGgtgt                                                                                                                        >  1:199530/1‑139 (MQ=255)            tAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGcccc                                                                                                                   <  2:329917/139‑1 (MQ=255)                   cATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCt                                                                                                            <  2:463395/139‑1 (MQ=255)                          cAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCa                                                                                                     <  2:553642/139‑1 (MQ=255)                             agGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAgcg                                                                                                  >  1:692713/1‑139 (MQ=255)                               gCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCt                                                                                                >  2:1018390/1‑139 (MQ=255)                                  gTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTaa                                                                                             >  2:809201/1‑139 (MQ=255)                                        cgcgTCGTGTTCGAACCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGc                                                                                       <  1:809201/139‑1 (MQ=255)                                                      aCCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGt                                                                         <  1:685812/139‑1 (MQ=255)                                                       ccGGCCCGTGGCGGGAATGCCGGGTGAAGCGCCCGGCACAAGGCCATGGCGGGCCATCACTTTATGTACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCCGCGCTTAATCTTGCGGGCTCCCCAGCGtt                                                                        <  2:687719/139‑1 (MQ=255)                                                          gCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCAt                                                                     >  2:911029/1‑139 (MQ=255)                                                          gCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCAt                                                                     >  1:699668/1‑139 (MQ=255)                                                           cccGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATg                                                                    >  1:252128/1‑139 (MQ=255)                                                                   gggAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGACGGTCAt                                                            <  1:1018390/139‑1 (MQ=255)                                                                       aTGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCtt                                                                                         <  1:255038/106‑1 (MQ=255)                                                                       aTGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCtt                                                                                         >  2:255038/1‑106 (MQ=255)                                                                          cccGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGTATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGACGGTCATGGGCCAt                                                     >  1:426418/1‑139 (MQ=255)                                                                                   gcacccGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGACGGTCATGGGCCATACGcagcag                                            <  2:936938/136‑1 (MQ=255)                                                                                    cgcCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGa                                                                   >  1:1092454/1‑115 (MQ=255)                                                                                    cgcCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGa                                                                   <  2:1092454/115‑1 (MQ=255)                                                                                       ccGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGACGGTCATGGGCCATACGCAGCAGGGcc                                        <  2:102088/139‑1 (MQ=255)                                                                                          gcagcaGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGACGGTCATGGGCCATACGCAGCAGGGCCGTg                                     <  2:199530/139‑1 (MQ=255)                                                                                                           gCCATCAGGTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGACGGTCATGGGCCATACGCAGCAGGGCCGTGATGTCGTCAGATGAGCg                    >  1:600093/1‑139 (MQ=255)                                                                                                                  ggTTATGGACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGACGGTCATGGGCCATACGCAGCAGGGCCGTGATGTCGTCAGATGAGCGGTTCggg             <  2:600093/139‑1 (MQ=255)                                                                                                                         gACGGTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGACGGTCATGGGCCATACGCAGCAGGGCCGTGATGTCGTCAGATGAGCGGTTCGGGGAATGGt      >  2:499947/1‑139 (MQ=255)                                                                                                                             gTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGACGGTCATGGGCCATACGCAGCAGGGCCGTg                                     <  1:713993/104‑1 (MQ=255)                                                                                                                             gTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGACGGTCATGGGCCATACGCAGCAGGGCCGTg                                     >  2:713993/1‑104 (MQ=255)                                                                                                                             gTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGACGGTCATGGGCCATACGCAGCAGGGCCGTGATGTCGTCAGATGa                       <  2:599683/118‑1 (MQ=255)                                                                                                                             gTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGACGGTCATGGGCCATACGCAGCAGGGCCGTGATGTCGTCAGATGa                       >  1:599683/1‑118 (MQ=255)                                                                                                                             gTGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGACGGTCATGGGCCATACGCAGCAGGGCCGTGATGTCGTCAGATGAGCGGTTCGGGGAATGGTGCgg  >  1:962297/1‑139 (MQ=255)                                                                                                                              tGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGACGGTCATGGGCCATACGCAGCAGGGCCGTGATGTCGTCAGATGAg                      <  2:552891/118‑1 (MQ=255)                                                                                                                              tGCTGAAGGC‑GGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGACGGTCATGGGCCATACGCAGCAGGGCCGTGATGTCGTCAGATGAg                      >  1:552891/1‑118 (MQ=255)                                                                                                                                        |                                                                                                                                 AAAGTGGCCCTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTGCCCCTGGTCCTCGAGCCAGCGCTTAATCTTGCGGGCTCCCCAGCGTTCATGACGGTCATGGGCCATACGCAGCAGGGCCGTGATGTCGTCAGATGAGCGGTTCGGGGAATGGTGCGG  >  NC_000913/281525‑281788

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑