Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	17,281	G→A	intergenic (+271/‑208)	sokC → / → nhaA	small regulatory RNA antitoxin SokC/Na(+):H(+) antiporter NhaA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	17,281	0	G	A	97.1%	98.6 / ‑6.8	34	intergenic (+271/‑208)	sokC/nhaA	small regulatory RNA antitoxin SokC/Na(+):H(+) antiporter NhaA
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (17/16);  total (18/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

AGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAATTATTACTTTTCCTAATTAATCCCTCAGGAATCCTCACCTTAAGCTATGATTATCTAGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAA‑CGCATCTCACCGCTGATGGCGCAAATTCTTCAATAGCTCGTAAAAAACGAATTATTCCTACACTATAATCTGATTTTAACGATGATTCGTGCGGGGTAAAATAGTAAAAACGATCTATTCACCTGAAAGAGAAATAAAAAGTGAAACATCTGCATCGATTCTTTAGCAGTGAT  >  NC_000913/17040‑17521                                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                                  agCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCTTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAATTATTACTTTTCCTAATTAATCCCTCAGGAATCCTCAc                                                                                                                                                                                                                                          >  2:12808/1‑251 (MQ=255)      aacacACCCGCCGCTATTATATCGCTCTCTTTAACCCATTCTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTaa                                                                                                                                                                                                                                     <  1:547729/247‑1 (MQ=255)             ccgccgCTATTATATCGCCCTCGTTAACCCATTCTGTTTTATCGATTCTAATCCTGAATACGCCGCGCAATTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTAt                                                                                                                                                                                                                                <  2:6746/249‑1 (MQ=255)                           tCGCTCTCTTTAACCCATTCTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCtt                                                                                                                                                                                                                  >  1:225794/1‑249 (MQ=255)                                                      tCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTc                                                                                                                                                                                     >  2:2369/1‑251 (MQ=255)                                                                    gAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCaaaaaactcatc                                                                                                                                                                         <  1:2369/249‑8 (MQ=255)                                                                                           cGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATAATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTAGCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAAttcttc                                                                                                                                                <  1:622597/251‑1 (MQ=255)                                                                                                      aaTGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGgc                                                                                                                                                           >  1:468635/1‑229 (MQ=255)                                                                                                      aaTGACTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGCCGACAAGCTTGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCTCCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGgc                                                                                                                                                           <  2:468635/229‑1 (MQ=255)                                                                                                          aTTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCAc                                                                                                                                                                                                                                          >  1:204659/1‑146 (MQ=255)                                                                                                          aTTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCAc                                                                                                                                                                                                                                          <  2:204659/146‑1 (MQ=255)                                                                                                                                      tttaTCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGAt                                                                                                     >  1:572770/4‑251 (MQ=255)                                                                                                                                                   ttGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGAtt                                                                                        >  1:66460/1‑251 (MQ=255)                                                                                                                                                     gacgacAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGAttt                                                                                       <  1:115968/250‑2 (MQ=255)                                                                                                                                                               tGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTa                                                                             >  1:283480/1‑250 (MQ=255)                                                                                                                                                                   ttattTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACACTGATTTGTGCGGGGTAAAAt                                                                         >  2:205449/1‑250 (MQ=255)                                                                                                                                                                      tttttGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCTCCTTAAGCTATGATTATCTGGGCTTAggg                                                                                                                                                                                                              <  2:10348/114‑1 (MQ=255)                                                                                                                                                                      tttttGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAggg                                                                                                                                                                                                              >  1:10348/1‑114 (MQ=255)                                                                                                                                                                              atatTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATAGTAAAAACGAt                                                             >  2:138053/1‑251 (MQ=255)                                                                                                                                                                                     cctaacaaataacGCCGACTGACAAGCAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATACTCTGATTTTAACGATGTTTTGTGCGGGGTAAAATAGTAAAAACGATCTATTc                                                       >  1:3109/13‑250 (MQ=255)                                                                                                                                                                                                acGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTTAGCTATGATTATCTGGGCTTAGGGTCACGCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAACTTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATAGTAAAAACGATCTATTCACCTGAAAgaga                                           <  1:249995/250‑1 (MQ=255)                                                                                                                                                                                                      aCTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATAGTAAAAACGATCTATTCACCTGAAAGAGAAATaaa                                     <  1:470459/251‑1 (MQ=255)                                                                                                                                                                                                         tacaagaAATTAATTTTTATTTTTCCTAATTAATCCCACAGAAAACCTCACCTTAAGTTATTATTATCTGTGCTTAGGTTCACTCATGAGCACTTACAGCCTTCAAAAAACTAAACTCACCGCTGATGGCGCAAATTCTTCAATTGATCGTAAAAAACGAGTTATTCCTACACTATAATCTTATATTAACGATAATTTGTACGATATAAAATAGTAAAAACGATCTATTCACCTGAAAtaaaaataaaaa                                   <  2:300693/249‑1 (MQ=255)                                                                                                                                                                                                         gacaagcaattaattATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATTGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATAGTAAAACCGATCTATTCACCTGAAAGAGAAATaaaaa                                   <  1:395651/243‑1 (MQ=255)                                                                                                                                                                                                             agaaaTTAATTATTTCTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGAGCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATa                                                                        <  2:218654/207‑1 (MQ=255)                                                                                                                                                                                                             agaaaTTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATa                                                                        >  1:218654/3‑209 (MQ=255)                                                                                                                                                                                                                   taattaTTACATTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTCAGATAGTAAAAACGATCTATTCACCTGAAGGAGAAGTAAAAAGTGAAACAtat                        >  2:290283/1‑249 (MQ=255)                                                                                                                                                                                                                              tttCCTAATAAATCCCTCAGAAAGTCGCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACGCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATGTGTGCGGGGTAAAAGAGTAAAAACGATCTATTCACCTGAAAGAGAAATAAAAAGTGAAACATCTGCATCGAtt               <  2:204489/249‑1 (MQ=255)                                                                                                                                                                                                                                      ttaatCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACgatg                                                                                           <  1:512273/165‑1 (MQ=255)                                                                                                                                                                                                                                      ttaatCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACgatg                                                                                           >  2:512273/1‑165 (MQ=255)                                                                                                                                                                                                                                      ttaatCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCgg                                                                                 <  1:292186/175‑1 (MQ=255)                                                                                                                                                                                                                                      ttaatCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCgg                                                                                 >  2:292186/1‑175 (MQ=255)                                                                                                                                                                                                                                       taatCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGACACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATAGTAAAAACGATCTATTCACCTGAAAGAGAAATAAAAAGTGAAACATCTGCATCGATTCTTTAGCAGTg    >  1:238315/1‑251 (MQ=255)                                                                                                                                                                                                                                         atCCCTCAGAAATACTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCCTCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATAGTAAAAACGATCTATTCACCTGAAAGAGAAATAAAAAGTGAAACATCTGCATCGATTATTTAGCAGTGAt  >  1:241281/1‑251 (MQ=255)                                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                                  AGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAATTATTACTTTTCCTAATTAATCCCTCAGGAATCCTCACCTTAAGCTATGATTATCTAGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAA‑CGCATCTCACCGCTGATGGCGCAAATTCTTCAATAGCTCGTAAAAAACGAATTATTCCTACACTATAATCTGATTTTAACGATGATTCGTGCGGGGTAAAATAGTAAAAACGATCTATTCACCTGAAAGAGAAATAAAAAGTGAAACATCTGCATCGATTCTTTAGCAGTGAT  >  NC_000913/17040‑17521

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑