Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,907,444	G→A	N45N (AAC→AAT)	phoU ←	negative regulator of the pho regulon

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,907,444	0	G	A	100.0%	75.1 / NA	26	N45N (AAC→AAT)	phoU	negative regulator of the pho regulon
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (11/15);  total (11/15)

ACGGCTGATGCTGCTGGGAGAATTTCTCCAGCGCAGTACGGCAGATTTTGTCCGCCACGTCGCCAATACGCTCCAGCTCGGCAATGGTTTTACTGATCACCATAACCAGTCGCAGGTCGCTCGCCGTCGGCTGACGTTTGGCGATAATGCGCACGCAGGCTTCATCGATCGCCACTTCCATCATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCGTTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTGGCTTGGT  >  NC_000913/3907209‑3907646                                                                                                                                                                                                                                            |                                                                                                                                                                                                           ncGGCTGATGCTGCTGGGAGAATTTCTCCAGCGCAGTACGGCAGATTTTGTCCGCCACGGCGCCAATACGCTCCAGCTCGGCAATGGTTTTACTGATCACCATAACCAGTCGCAGGTCGCTCGCCGTCGGCTGACGTTTGGCGATAATGCGCACGCAGGCTTCATCGATCGCCACTTCCATAATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTATGCATCGCGGTg                                                                                                                                                                                             >  1:112197/2‑251 (MQ=255)          gctgctGGGAGAATTTCTCCAGCGCAGTACGGCAGATTTTGTCCGCCACGTCGCCAATACGCTCCAGCTCGGCAATGGTTTTACTGATCACAATAACCAGTCGCAGGTCGCTCGCCGTCGGCTGACGTTTGGCGATAATGCGCACGCAGGCTTCATCGATCGCCACTTCCATCATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTATGCATCGCGGTGATTGCATc                                                                                                                                                                                     >  1:245613/1‑250 (MQ=255)                nggAGAATTTCTCCAGCGCAGTACGGCAGATTTTGTCCGACACGTCGCCAATACGCTCCAGCTCGGCAATGGTTTTACTGATCACCATAACCAGTCGCAGGTCGCTCGTCGTCGGCTGACGTTTGGCGATAATGCGCACGCAGGCTTAATCGATCGCCACTTCCATCATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTATGCATCGCGGTGATTGCATCAGaa                                                                                                                                                                                 >  1:39660/2‑248 (MQ=255)                                                                     cGCTCCAGCTCGGCAATGGTTTTACTGATCAACATAACCAGTCGCAGGTCGCTCGCCGTCGGCTGACGTTTGCCGCTAATGCGCACGCAGGCTTCATCGATCGACACTTCCCTCATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGATGTCCTGATTATGCATCGCGGTGATTGCATCAGAACGCTGCTGCTCCACCATGCCGCCCATGGTCATCCCCTGCGTGCGGATCCTTTcc                                                                                                                           >  1:314609/1‑249 (MQ=255)                                                                         ccAGCTCGGCAATGGTTTTACTGATCACCATAACCAGTCGCAGGTCGCTCGCCGTCGGCTGACGTTTGGCGATAATGCGCACGCAGGCTTCATCGATCGCCACTTCCATCATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGtt                                                                                                                       <  1:364002/249‑1 (MQ=255)                                                                              tCGGCAATGGTTTTACTGATCACCATAACCAGTCGCAGGTCGCTCGCCGTCGGCTGACGTTTGGCGATAATGCGCACGCAGGCTTCATCGATCGCCACTTCCATCATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTATGCATCGCGGTGATTg                                                                                                                                                                                         <  1:22297/178‑1 (MQ=255)                                                                                      ggTTTTACTGATCACCATAACCAGTCGCAGGTCGCTCGCCGTCGGCTGACGTTTGGCGATAATGCGCACGCAGGCTTCATCGATCGCCACTTCCATCATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTATGCAGCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCGTTGAACTggn                                                                                                        <  1:42212/251‑2 (MQ=255)                                                                                                          ncAGTCGCAGGTCGCTCGCCGTCGGCTGACGTTTGGCGATAATGCGCACGCAGCCTTCATCGATCGCCACTTCCATCATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTATGCATCGCGGTGCTTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCGTTGAACTGGCCGGAAATATGTttatta                                                                                       >  1:85786/2‑248 (MQ=255)                                                                                                                            cnGTCGGCTGACGTTTGGCGATAATGCGCACGCAGGCTTCATCGATCGCCACTTCCATCATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCGTTGAACTGGCCg                                                                                                      >  1:349482/1‑215 (MQ=255)                                                                                                                                 ggCTGNNGTNNNGCNNTAATGCGCACGCAGGCTTCATCGNTCGCCACTTCCATCATGTTGACGTTCTTGNCNCNTTCGNNGACNCGCTTCGCCANATCGCTGTCCTGATTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGNTncacc                                                                                                                                                                  >  2:335463/1‑150 (MQ=255)                                                                                                                                 ggCTGACGTTTGGCGATAATGCGCACGCAGGCTTCATCGATCGCCACTTCCATCATGTTGACGTTCTTGTCTCCTTCGATGACGCGCTTCGCCATAGCGCTGTCCTGATTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTccacc                                                                                                                                                                  <  1:335463/150‑1 (MQ=255)                                                                                                                                  gCTGACGTTTGGCGATAATGCGCACGCAGGCTTCATCGATTCCCACTTACATACTCTTGACGTTCTTGTCGCCATCGATGAAGCGATTAGCCAGACCGCTGTCCTGATTATGCATCGCGGAGATTGCATCAGAAAGCTGCTGCTCCACAATGCCGCCCATGGTCATCACATGCGTGCGGATACTTTCCAGTTCGGCGTTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTcc                                                            >  1:241798/1‑251 (MQ=255)                                                                                                                                        gTTTGGCGATAATGCGCACGCAGGCTTCATCGATCGCCACTTCCATCATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTATGCATCTCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCGTTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCa                                                                       <  1:192452/234‑1 (MQ=255)                                                                                                                                             gCGATAATGCGCACGCAGGCTTCATCGATCGCCACTTCCATCATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCGTTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCg                                                 >  1:161820/1‑251 (MQ=255)                                                                                                                                                  aaTGCGCACGCAGGCTTCATCGATCGCCACTTCCATCATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCCGATCGCTGTCCTGATTATGCATCGCGGTGATTGCATCAGAAAGCGGCTGCTCCACCATTCCGCCCATGGTCCTCACCTGCGTGCGGTAACTTCCCAGTTCGGGTTTTAACTGGCCGGAAAGAGGTTTATTAATAATGAGACGGTCCATAACGCACTCCTGAATCAACCGTAAc                                             <  1:406574/250‑1 (MQ=255)                                                                                                                                                      cgcacgcaGGCTTCATCGATCGACACTTCCATCATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGATCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCGTTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCg                                        >  1:161555/1‑251 (MQ=255)                                                                                                                                                            caGGCTTCATCGATCGCCACTTCCATCATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCGTTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTa                                               >  1:149254/1‑238 (MQ=255)                                                                                                                                                                       gatcgCCACTTCCNTNATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGNCCTGATTATGNATCNNGGTGNTNGNATCAGAAAGCTTCTGCTCCACCATGCCGCNCATGGTCATCACCTGCGTGCGGANNCTNNNCANNTCGGc                                                                                                                   <  2:327423/159‑1 (MQ=255)                                                                                                                                                                        atcgCCACTTCCATCATGTTGACGTGCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTAGGCAGCGCGGTTAGTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCtgc                                                                                                                                          <  1:193363/135‑1 (MQ=255)                                                                                                                                                                            ccACTTCCATCATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTGCCAGTTCGGCGTTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAAcc                                                  <  1:69528/219‑1 (MQ=255)                                                                                                                                                                            ccACTTCCATCATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCGCCACCATGCCGCCCATGGTCTTCACCTGCGTGCGGATACTTTCCAGtt                                                                                                                       <  1:372241/150‑1 (MQ=255)                                                                                                                                                                                  ccATCATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCGTTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCg            <  1:290531/251‑1 (MQ=255)                                                                                                                                                                                       atGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCGTTGAACTGTCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTGGc       <  1:320277/251‑1 (MQ=255)                                                                                                                                                                                            gACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCGTTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTGGCTTgg   <  1:167638/250‑1 (MQ=255)                                                                                                                                                                                                 tCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGATTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCGTTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGCTGATGTAGTCTTCTGTTTGTTTCTTCGCTg         <  1:352839/239‑1 (MQ=255)                                                                                                                                                                                                                                atctcTGTCCTGATTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCGCCACCATGCCGCCCATAGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCGTTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAAGCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTGGCTTGGt  <  1:447706/211‑1 (MQ=255)                                                                                                                                                                                                                                            |                                                                                                                                                                                                           ACGGCTGATGCTGCTGGGAGAATTTCTCCAGCGCAGTACGGCAGATTTTGTCCGCCACGTCGCCAATACGCTCCAGCTCGGCAATGGTTTTACTGATCACCATAACCAGTCGCAGGTCGCTCGCCGTCGGCTGACGTTTGGCGATAATGCGCACGCAGGCTTCATCGATCGCCACTTCCATCATGTTGACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCGTTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTGGCTTGGT  >  NC_000913/3907209‑3907646

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑