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	88.9%	39.7 / ‑0.7	18	T156T (ACT→ACC)	phoP	DNA‑binding transcriptional dual regulator PhoP
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base G (9/7);  total (10/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.11e-01

AGCGAGAGCGGGAAAAAAAGACGCAGTAATTTTTTCATCAGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATAGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAA  >  NC_000913/1189739‑1190216                                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                             aGCGAGAGCGGGAAAAAAAGACGCAGTAATTTTTTCATCAGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCg                                                                                                                                                                                                                                     <  1:70724/251‑1 (MQ=255)          gggAAAAAAAGACGCAGTAATTTTTTCATCAGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTc                                                                                                                                                                                                                            >  1:49256/1‑251 (MQ=255)           ggAAAAAAAGACGCAGTAATTTTTTCATCAGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCAATAATGGTGTATTCGAACGCGGTc                                                                                                                                                                                                                            >  1:292057/1‑250 (MQ=255)                                     atcaGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGGGGTAATCACTTCTTGGGGTTATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAAt                                                                                                                                                                                                     >  1:196073/1‑247 (MQ=255)                                        aGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAAt                                                                                                                                                                                              <  1:124082/251‑1 (MQ=255)                                                                                          tGGGGATTTTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGGATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCTCGTTGCCATTATTGCTTATCAACGGTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTGCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCtg                                                                                                                                               <  2:196073/248‑1 (MQ=255)                                                                                          tGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCtgtg                                                                                                                                             >  1:54129/1‑250 (MQ=255)                                                                                                                                               ggTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATAACTTCGTCATTAATAGATAATTCACGGCGAGAGAGCTCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCTCGCCATCACCTCtt                                                                                       >  1:267551/1‑251 (MQ=255)                                                                                                                                                             gCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTaa                                                                                                                 <  1:170446/211‑1 (MQ=255)                                                                                                                                                                     gCATCCGGATAGATTTGGAGCAATAACGAATCTTTGCTGACCCCTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTTTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTGCAATATGAAACGGTTTAGTcac                                                                 <  1:47968/251‑1 (MQ=255)                                                                                                                                                                        tCCGGATAGAGCTGGATCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGGCAGTTTGATCACTTCGTCATTAATAGATAATTCACGTCGGGCGAGATCAACCTTAATCCGGGGGAGCGAAATGACCTGTGCAGCAAGACCGCTATTACGCAGCATTAATGCCTGCATTCGCGTCATCACCTCTTCACTATGAAACGGTTTAGTcactt                                                               >  2:241513/1‑248 (MQ=255)                                                                                                                                                                                     ggAGCATTAACGAATCTTTGCTTGCCACTTTGCCATTATTGCGTTTCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCAcc                                                  <  2:278543/250‑1 (MQ=255)                                                                                                                                                                                      gAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCgg                                                <  1:217893/251‑1 (MQ=255)                                                                                                                                                                                                           gACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGCACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGt                           >  1:254442/1‑251 (MQ=255)                                                                                                                                                                                                                     ccATTATTGCGTATCAACGTTTCCATAATGGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGCAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCt                 >  1:140063/1‑251 (MQ=255)                                                                                                                                                                                                                       attattGCGTATCAACGTTTCCATAATAGTGTATTCGAACGCTGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAGACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCttt               >  1:59341/1‑251 (MQ=255)                                                                                                                                                                                                                         tattGCGTAAAAACGTTCCCATAATGGTGTATTCGCAAGCGGTCAGATTGATAAATTCGTCATTACTAGCTAATTCACGGCGAGACAGATCAAACTGAAACGGGGGGAGCGAAATGACCTGTGAAGCAAGACCGCTATTACGACGCATTAATGCCTGCATTCGCGCCCTCCACTATTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATAATTCGAATTTGTCCTGCCAGCTTTcc             >  2:133169/1‑250 (MQ=255)                                                                                                                                                                                                                                    aaCGGTTCCATAATAGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATGCACGGCGAGAGAGATCAACCTGAGACGGGGGGAGCGAAATGACCTGTGAAGCCAGTCCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAAGCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTaa  <  1:34135/251‑1 (MQ=255)                                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                             AGCGAGAGCGGGAAAAAAAGACGCAGTAATTTTTTCATCAGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGGCTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATAGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAA  >  NC_000913/1189739‑1190216

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑