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	90.9%	51.9 / ‑3.1	22	T156T (ACT→ACC)	phoP	DNA‑binding transcriptional dual regulator PhoP
Reads supporting (aligned to +/- strand):  ref base A (0/2);  new base G (11/9);  total (11/11)
Fisher's exact test for biased strand distribution p-value = 4.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.21e-01

CCGCAGCGAGAGCGGGAAAAAAAGACGCAGTAATTTTTTCATCAGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGG‑CTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAAT‑AGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTA  >  NC_000913/1189735‑1190176                                                                                                                                                                                                                                                        |                                                                                                                                                                                                     ccGCAGCGAGAGCGGGAAAAAAAGACGCAGTAATTTTTTCATCAGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGGGCATCAATGGTATGG‑CTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAAT‑GGTGTa                                                                                                                                                                                                 <  1:277038/251‑1 (MQ=255)                gAAAAAAAGACGCAGTAATTTTTTCATCAGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGG‑CTTTCCCGCAGCTCCGCATCCGGATAGATTTGGAGCATTAACGGATCTTTGCTGACTACTTTGCCATTATTGCGTAGCAACGTTTCCATAAT‑GGTGTATTCGAACGCGGTCAg                                                                                                                                                                                  <  1:374295/251‑1 (MQ=255)                 aaaaaaaGACGCAGTAATTTTTTCATCAGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGG‑CTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAAT‑GGTGTATTCGAACGCGGTCAGt                                                                                                                                                                                 >  1:33988/1‑251 (MQ=255)                       aGACGTAGTAATTATTTCATACGCGGAATTCGTATAGATAGCCCTGGCCGCGAACGGTGGTAATTACTTCTTTGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGG‑CTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAAT‑AGTGTATTCGAACGCGGTCAGTTTGATc                                                                                                                                                                           <  2:111167/251‑1 (MQ=255)                              gTAATTTTTTCATCAGCGCAATTCGACCAGATAGCCCTGGCAGCGAACGGTGGAAATCAATTCTTGGGGCTATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGG‑CTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGTATTAACGAATCTTTGCGGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAAT‑GGTGTTTTCGCACGCGGTCAGTTTAATCACTTCGt                                                                                                                                                                    >  2:355612/1‑251 (MQ=255)                                 aTTTTTTCATCAGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGG‑CTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAAT‑GGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCAt                                                                                                                                                                 <  1:50325/251‑1 (MQ=255)                                         atcagagcaattctagctgtgtgCCCTGGTCGCGAACGAGGGTAATCGATTCTTGGGGAAATTGTGCCTGAAGTTTTTTGCGCAGACGGCCCATTAGTGCATCAATGGTATGG‑CTTCCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCATTTTGCCATTATTTCGTATCAACGTTTCCATAAT‑GGTGTAGTCGAACGCGGTCAGTTTGATCACTGCGTCATTAATAgct                                                                                                                                                         <  2:165604/229‑3 (MQ=255)                                           caGCGCAATGCGAACAGATATCCCTTGCCGCTAACTGTGGTAATCACTTCTTTGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGT‑CTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAAT‑GGTGGATTCGAACGCGGTCAGTTTGATCCCTTCGTCATTAAGAGATa                                                                                                                                                        <  2:113334/250‑1 (MQ=255)                                                                cccTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGG‑CTTTACCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAAT‑GGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAAATAATTCACGGCGAAAGAGGTCAAc                                                                                                                                  >  2:274927/1‑251 (MQ=255)                                                                   tGGCCGCGAACGGCGGTAATCACTTCTTGGGGATATTGCGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGG‑CTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAAT‑GGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTg                                                                                                                               >  1:114087/1‑251 (MQ=255)                                                                        gcgAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGG‑CTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAAT‑GGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACg                                                                                                                          <  1:245317/251‑1 (MQ=255)                                                                           aaCGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGAATGG‑CTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAAT‑GGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGCTCAACCTGAAACgggg                                                                                                                       >  1:246701/1‑251 (MQ=255)                                                                                                       ttgtcctgattttggtttcgcAGACGTCACATCAGTACATCAATG‑TCTGGTCTGTCCCGCTGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCAATTTGCCATGATTGCGTATCAACGTTTTCATAAG‑GGTGTATTCGAACGCGGTCAGTCTGATCTCTTCGGCATTAATAGATAATTCACGACGATAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTTTGAAGCCatac                                                                                            <  2:19021/232‑4 (MQ=255)                                                                                                                                 tCCCATCAGTACATCAATGGTATGG‑CTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAAT‑GGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGc                                                                  >  1:141246/1‑250 (MQ=255)                                                                                                                                             aTCAATGGTATGG‑CTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAAT‑GGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATc                                                      >  1:345385/1‑250 (MQ=255)                                                                                                                                                aaTGGTATGG‑CTTTCCCGCAGCTCCGCATCCGGATAGAGTTTGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTTCATAAT‑GGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACct                                                  <  1:161653/251‑1 (MQ=255)                                                                                                                                                    gTATGG‑CTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAAT‑GGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTc                                              >  1:130993/1‑251 (MQ=255)                                                                                                                                                               cctcccgtgccGCTTCCGGATAGAGTTGGAGTCTTAAGTAATCTTTGCTGCCTCCCATGCCATTATTGTGTATCAACGGTTCCATAATGAG‑GTATTCGAACGCGGTCAGTTTGATCGCTTCGTCATTAATAGATAATTCACGGCGAGATAGAGCCTCCTGAAGCGGGGGGAGCGAACTGACCTGTGAAGGCAGACCGCTATTACGACGCATTAAGGCCTGCATTCGCGCCATCACCTCTTCAATATGaaa                                     <  2:24690/241‑1 (MQ=255)                                                                                                                                                                            ttCCGGATAGTGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAAT‑GGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATCGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGACGCGAAATGCCCTGTGAAGCCAGACCGCTATTACGCCGCATTAAGGCCTGAATTCGCGCCATCACCTCTTCAATATGACCCGGTTTAGTCACAt                       >  2:94562/2‑251 (MQ=255)                                                                                                                                                                                           gAGCATTAACGAATCTTGTCTGCCCACCTTGCCATTAGTGTGGATCAATGTTTCCATAAT‑GGTGTATTCGAACGCGGTCAGTTTGATCACTTCGGCATTAATAGATAATTCACGGCTAGAGAGATCAACCTGAAACGGTGGGAGCGAAATGACCTGTGAAGCCAGATCGCTAGTACGCCGCATTAATGCCTGCATTCGCGCCAGCACCTCTTCAATAGGAAACGGTTTAGTCACCTAATCTTCAGCACCgg        <  2:114087/251‑1 (MQ=255)                                                                                                                                                                                            aGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAAT‑GGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGc       >  1:362574/1‑251 (MQ=255)                                                                                                                                                                                                  aaCGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAAT‑GGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGTGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCCTTCGCGCCATCACCTCTTCAATATGACACGGTTTAGTCACATAATCATCAGCACCGTCACTTa  >  1:125267/1‑250 (MQ=255)                                                                                                                                                                                                                                                        |                                                                                                                                                                                                     CCGCAGCGAGAGCGGGAAAAAAAGACGCAGTAATTTTTTCATCAGCGCAATTCGAACAGATAGCCCTGGCCGCGAACGGTGGTAATCACTTCTTGGGGATATTGTGCCTGAATTTTTTTGCGCAGACGTCCCATCAGTACATCAATGGTATGG‑CTTTCCCGCAGCTCCGCATCCGGATAGAGTTGGAGCATTAACGAATCTTTGCTGACCACTTTGCCATTATTGCGTATCAACGTTTCCATAAT‑AGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTA  >  NC_000913/1189735‑1190176

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑