Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,189,980	A→G	T156T (ACT→ACC)	phoP ←	DNA‑binding transcriptional dual regulator PhoP

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,189,980	0	A	G	100.0%	86.6 / NA	27	T156T (ACT→ACC)	phoP	DNA‑binding transcriptional dual regulator PhoP
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (16/11);  total (16/11)

CCCGCAGCGAGAGCGGGAAAAAAAGACGCAGTAATTTTTTCATCAGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATAGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACC  >  NC_000913/1189734‑1190220                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                 cccGCAGCGAGAGCGGGAAAAAAAGACCCAGTAATTTTTTCACCAGCGCAATTCGAACAGATAGCCCTGACCGCGAACGGTGGTAATCACTTCTTGGTGATATTGTGCCTGAATTTTTTTTCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCATCTCCGCATCCGGATAGAGTTATAGCATTAACGAATCTTTGCTTACCACTTTACCATTATTGCGTATCATCGTTTCCATAATGgtgt                                                                                                                                                                                                                                              <  2:172155/251‑1 (MQ=255)                  aaaaaaaGTCGCAGTAATTTTTTCATCAGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGTATTAACGAATCTTTGCTGACCACTTTGCCATTATTTCTTATCAACGTGTCCATAATGGTGTATTCGAACGCGGTCAGt                                                                                                                                                                                                                             <  1:140742/251‑1 (MQ=255)                      aaaGACGCAGTAATTTTTTCATAAGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGACTTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATCATGGTGTATTCGAACGAGGTCAGTTTg                                                                                                                                                                                                                          >  1:313357/1‑250 (MQ=255)                       aaGACGCAGTAATTTTTTCATCAGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGAt                                                                                                                                                                                                                        >  2:158529/1‑251 (MQ=255)                                    tttttCATCAGCTCTATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAAGGGTATGGCTTTCCCGCAGCTCCGCATACGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCTTAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCAtt                                                                                                                                                                                                            <  2:317778/250‑1 (MQ=255)                                       ttCATCAGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAAt                                                                                                                                                                                                         >  1:348524/1‑250 (MQ=255)                                                      cGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCg                                                                                                                                                                                          <  1:88439/250‑1 (MQ=255)                                                                     ggCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTAACGGCGAGAGAGCTCAACCTg                                                                                                                                                                           >  2:272320/1‑250 (MQ=255)                                                                     ggCCGCGAAAGGAGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTACCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGAGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATAAACCTg                                                                                                                                                                           >  2:272332/1‑250 (MQ=255)                                                                           ggacggaagtAATCACTTTTTGGGGATGTTATGCATGAATTTTTTTGCGCAGACGTCACATCAGTACATCAATGTTATGGCTTTCCCGCAGCACCACATCCGGATAGAGTTGGAGAATTAACGAATCTTTGCTGACCACTTTGCCATTAATGCGTATCAACGTTTCCATAATGGTGGATTCGAACGCGGTATGTTTGATCACTTCGTACTTAATAGATAATTCACGGCGAGAGAAATCAACCTTGAACggg                                                                                                                                                                    >  2:44361/9‑251 (MQ=255)                                                                                  ggtAATCACTTCTTGGGGATATTGTGCCTGAATTTGTTCGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATGAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCg                                                                                                                                                             <  2:190809/251‑1 (MQ=255)                                                                                                             cTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCACCGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGCGAGAGATCAACCTGACACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTAt                                                                                                                                  >  1:1/1‑251 (MQ=255)                                                                                                                 aTTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACAGCTATTAcg                                                                                                                              >  1:302030/1‑251 (MQ=255)                                                                                                                              gACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGcc                                                                                                                 <  1:158529/251‑1 (MQ=255)                                                                                                                               aCGTACCATCAGTACAGCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTAGTCGAACGCGGTCAGGTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCt                                                                                                                <  2:1/251‑1 (MQ=255)                                                                                                                                        cAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTcgcg                                                                                                       >  1:120249/1‑251 (MQ=255)                                                                                                                                            actgcAATGGTATGGCTTTCCCGCAGGTCCGCCTCCGGATATAGTTGGAGCATTAACGAATCTTGTCTGACCACTTTGCCATTATTGCGTATCAACGTTTCTATAATGGTTTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGTGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCTCATTAATGCCTGCATTCCCGCCa                                                                                                    <  2:121705/246‑1 (MQ=255)                                                                                                                                                    ggTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACctct                                                                                            <  2:120249/250‑1 (MQ=255)                                                                                                                                                      tATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTc                                                                                          >  1:102287/1‑250 (MQ=255)                                                                                                                                                                        ccGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTc                                                                       >  1:115793/1‑251 (MQ=255)                                                                                                                                                                           cATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTcac                                                                     >  1:224974/1‑250 (MQ=255)                                                                                                                                                                                ggATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGGGTATTCGAACGCGGTCAGTTTGATCGCTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGGATTCGCGCCATCACCTCTGCTATATGAAACGGTTTAGTCACATAatc                                                               <  1:144117/251‑1 (MQ=255)                                                                                                                                                                                      agTTGGAGCATTAACGAATCTTTGCTGCCCACTTTGCCATTATTGCGTCTCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTATGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCCCATAATCATCAGc                                                         >  1:264496/1‑251 (MQ=255)                                                                                                                                                                                             gCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGCACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCACGCCATCACCTCTTCAATATGAACCGGTTTAGTCCCATAATCATCAGCACCGGcc                                                  >  2:170104/1‑250 (MQ=255)                                                                                                                                                                                                  aaCGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTa                                              >  1:97215/1‑250 (MQ=255)                                                                                                                                                                                                                         gCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGAACCGGAACTTAATACTTCGACTTTGTCCTGCCAGc                      >  2:21762/1‑251 (MQ=255)                                                                                                                                                                                                                                              ttCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACGTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGGGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCTCTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATAcc  <  2:224974/250‑1 (MQ=255)                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                 CCCGCAGCGAGAGCGGGAAAAAAAGACGCAGTAATTTTTTCATCAGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATAGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACC  >  NC_000913/1189734‑1190220

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑