Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	17,348	(A)5→6	intergenic (+338/‑141)	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	17,348	1	.	A	93.3%	85.6 / ‑0.6	30	intergenic (+338/‑141)	sokC/nhaA	small regulatory RNA antitoxin SokC/Na(+):H(+) antiporter NhaA
Reads supporting (aligned to +/- strand):  ref base . (2/0);  new base A (17/11);  total (19/11)
Fisher's exact test for biased strand distribution p-value = 5.20e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

GAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAATTATTACTTTTCCTAATTAATCCCTCAGGAATCCTCACCTTAAGCTATGATTATCTAGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑A‑C‑GCATCTCACCGCTGATGGCGCAAATTCTTCAATAGCTCGTAAAAAACGAATTATTCCTACACTATAATCTGATTTTAACGATGATTCGTGCGGGGTAAAATAGTAAAAACGATCTATTCACCTGAAAGAGAAATAAAAAGTGAAACATCTGCATCGATTCTTTAGCAGTGATGCCTCGGGAGGCATTATTCTTATCATTGCCGCTATCCTGGCGATGATTATGG  >  NC_000913/17107‑17573                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                   gAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCaaaa‑aactcatc                                                                                                                                                                                                                              <  1:2369/249‑8 (MQ=255)                        cGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATAATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTAGCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAAttcttc                                                                                                                                                                                                    <  1:622597/251‑1 (MQ=255)                                   aaTGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGgc                                                                                                                                                                                                               >  1:468635/1‑229 (MQ=255)                                   aaTGACTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGCCGACAAGCTTGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCTCCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGgc                                                                                                                                                                                                               <  2:468635/229‑1 (MQ=255)                                                                   tttaTCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGAt                                                                                                                                                         >  1:572770/4‑251 (MQ=255)                                                                                ttGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGAtt                                                                                                                                            >  1:66460/1‑251 (MQ=255)                                                                                  gacgacAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGAttt                                                                                                                                           <  1:115968/250‑2 (MQ=255)                                                                                            tGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTa                                                                                                                                 >  1:283480/1‑250 (MQ=255)                                                                                                ttattTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACACTGATTTGTGCGGGGTAAAAt                                                                                                                             >  2:205449/1‑250 (MQ=255)                                                                                                           atatTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATAGTAAAAACGAt                                                                                                                 >  2:138053/1‑251 (MQ=255)                                                                                                                  cctaacaaataacGCCGACTGACAAGCAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATACTCTGATTTTAACGATGTTTTGTGCGGGGTAAAATAGTAAAAACGATCTATTc                                                                                                           >  1:3109/13‑250 (MQ=255)                                                                                                                             acGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTTAGCTATGATTATCTGGGCTTAGGGTCACGCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAACTTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATAGTAAAAACGATCTATTCACCTGAAAgaga                                                                                               <  1:249995/250‑1 (MQ=255)                                                                                                                                   aCTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATAGTAAAAACGATCTATTCACCTGAAAGAGAAATaaa                                                                                         <  1:470459/251‑1 (MQ=255)                                                                                                                                      tacaagaAATTAATTTTTATTTTTCCTAATTAATCCCACAGAAAACCTCACCTTAAGTTATTATTATCTGTGCTTAGGTTCACTCATGAGCACTTACAGCCTTCAAAA‑AAC‑TAAACTCACCGCTGATGGCGCAAATTCTTCAATTGATCGTAAAAAACGAGTTATTCCTACACTATAATCTTATATTAACGATAATTTGTACGATATAAAATAGTAAAAACGATCTATTCACCTGAAAtaaaaataaaaa                                                                                       <  2:300693/249‑1 (MQ=255)                                                                                                                                      gacaagcaattaattATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATTGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATAGTAAAACCGATCTATTCACCTGAAAGAGAAATaaaaa                                                                                       <  1:395651/243‑1 (MQ=255)                                                                                                                                          agaaaTTAATTATTTCTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGAGCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATa                                                                                                                            <  2:218654/207‑1 (MQ=255)                                                                                                                                          agaaaTTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATa                                                                                                                            >  1:218654/3‑209 (MQ=255)                                                                                                                                                taattaTTACATTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTCAGATAGTAAAAACGATCTATTCACCTGAAGGAGAAGTAAAAAGTGAAACAtat                                                                            >  2:290283/1‑249 (MQ=255)                                                                                                                                                           tttCCTAATAAATCCCTCAGAAAGTCGCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACGCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATGTGTGCGGGGTAAAAGAGTAAAAACGATCTATTCACCTGAAAGAGAAATAAAAAGTGAAACATCTGCATCGAtt                                                                   <  2:204489/249‑1 (MQ=255)                                                                                                                                                                   ttaatCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACgatg                                                                                                                                               <  1:512273/165‑1 (MQ=255)                                                                                                                                                                   ttaatCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACgatg                                                                                                                                               >  2:512273/1‑165 (MQ=255)                                                                                                                                                                   ttaatCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCgg                                                                                                                                     <  1:292186/175‑1 (MQ=255)                                                                                                                                                                   ttaatCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCgg                                                                                                                                     >  2:292186/1‑175 (MQ=255)                                                                                                                                                                    taatCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGACACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATAGTAAAAACGATCTATTCACCTGAAAGAGAAATAAAAAGTGAAACATCTGCATCGATTCTTTAGCAGTg                                                        >  1:238315/1‑251 (MQ=255)                                                                                                                                                                      atCCCTCAGAAATACTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCCTCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATAGTAAAAACGATCTATTCACCTGAAAGAGAAATAAAAAGTGAAACATCTGCATCGATTATTTAGCAGTGAt                                                      >  1:241281/1‑251 (MQ=255)                                                                                                                                                                            cagaaaTCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑A‑CCTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGGTATTCCTCCACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATAGTAAAAACGATCTATTCACCTGAAAGAGAAATAAAAAGTAAAACATCTGCATCGATTCTTTAGCAGTGATGACTCg                                                >  1:631843/5‑251 (MQ=255)                                                                                                                                                                                            aaGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATAGTAAAAACGATCTATTCACCTGAAAGAGAAATAAAAAGTGAAACATCTGCATCGATTCTTTAGCAGTGATGCCTCGGGAGGCATTATTCtt                                 >  1:597271/1‑250 (MQ=255)                                                                                                                                                                                                        tctgggCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATAGTACAAACGATCTATTCACCTGAAAGAGAAATAAAAAGTGAAACATCTGCATCGATTCTTTAGCAGTGATGCCTCGGGAGGCATTATTCTTATCATTGCCGCt                     >  1:273351/5‑250 (MQ=255)                                                                                                                                                                                                                  gggTCACTCGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTATAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATAGTAAAAACGATCTATTCACCTGAAAGAGAAATAAAAAGTGAAACATCTGCATCGATTCTTTAGCAGTGATGCCTCGGGAGGCATTATTCTTATCATTGCCGCTATCCTGGCgat          >  1:502311/1‑251 (MQ=255)                                                                                                                                                                                                                       aCTCGTGAGCGCTTACAGCCGTAAAAATA‑C‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGATATTCCTACACTATAATCTGATTTTAAAGATGATTTGTGCGGGGTAAAATAGTAAAAACGATCTATTCACCTGAAAGAGAAATAAAAAGTGAAACATCTGCATAGCTTCTTTAGCAGTGATGACTCGGGAGGCATTATTATTATCATTGCCGCTCTCCTGGAGATGAttt     >  2:416918/1‑250 (MQ=255)                                                                                                                                                                                                                          cGTGAGCGCTTACAGCCGTCAAAA‑AAC‑TCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTACACTCTAATCTGATTTTAACGATGATTTGTGCGGGGTAAAATAGTAAAAACGATCTATTCACCTGAAAGAGAAATAAAAAGTGAAACATCTGCATCGATTCTTTAGCAGTGATGCCTCGGGAGGCATTATTCTTATCATTGCCGCTATCCTGGCGATGATTATgg  >  2:308093/1‑251 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                   GAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAATTATTACTTTTCCTAATTAATCCCTCAGGAATCCTCACCTTAAGCTATGATTATCTAGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAA‑A‑C‑GCATCTCACCGCTGATGGCGCAAATTCTTCAATAGCTCGTAAAAAACGAATTATTCCTACACTATAATCTGATTTTAACGATGATTCGTGCGGGGTAAAATAGTAAAAACGATCTATTCACCTGAAAGAGAAATAAAAAGTGAAACATCTGCATCGATTCTTTAGCAGTGATGCCTCGGGAGGCATTATTCTTATCATTGCCGCTATCCTGGCGATGATTATGG  >  NC_000913/17107‑17573

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: ‑