Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	17,175	C→T	intergenic (+165/‑314)	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	17,175	0	C	T	100.0%	114.2 / NA	36	intergenic (+165/‑314)	sokC/nhaA	small regulatory RNA antitoxin SokC/Na(+):H(+) antiporter NhaA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (22/14);  total (22/14)

AAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAATTATTACTTTTCCTAATTAATCCCTCAGGAATCCTCACCTTAAGCTATGATTATCTAGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAA‑CGCATCTCACCGCTGATGGCGCAAATTCTTCAATAGCTCGTAAAAAACGAATTATTCCTAC  >  NC_000913/16934‑17409                                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                            aaGAGGCACTCTACATGTGTTCAGCATATAGGGGGCCTCGGGTTGATAGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGATAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTCTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAatt                                                                                                                                                                                                                                    >  1:291636/1‑251 (MQ=255)            tACATGTGTTCAGCATATAGGGGGCCTCGGGTTGATAGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGATAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTCTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACa                                                                                                                                                                                                                          >  1:51532/1‑250 (MQ=255)                                      tCGGGTTGATAGTAAAATATCCCTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGATAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTCTGTTTTATCGATTCTAATCCTGACGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGCTTATTTTTGAAATCTTgtcc                                                                                                                                                                                               >  2:124606/1‑248 (MQ=255)                                         ggTTGATAGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGATAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTCTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTa                                                                                                                                                                                             >  1:24580/1‑250 (MQ=255)                                                        atCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGATAGCCTCAAGCACCCGCCGCTCTTATATCGCTCTATTTAACCCATTCTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACt                                                                                                                                                                             >  2:624850/1‑251 (MQ=255)                                                                                    ttCAGCTAATGCCTGAGACAGATAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTCTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCt                                                                                                                                                  >  1:342360/1‑250 (MQ=255)                                                                                          tAATGCCTGAGACAGATAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTCTGTTTTATCGATTCTACTCCTGAAGACGACTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGTCAAGCTGGATTATTTTTGAAATATTGTCATAACAAATAACGCCGACTGACAAGAAATTACTTATTACTTTTCCtaattaat                                                                                                                                           >  1:95923/1‑251 (MQ=255)                                                                                                    gacagataGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTCTGTTTTATCGATTCTAATCCTGACGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAgaa                                                                                                                                  >  2:531747/1‑248 (MQ=255)                                                                                                                cAAGCCCCCGCCGCTATTATATCGCTCTCTT‑AACCCATTCTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAg                                                                                                                    <  1:70291/251‑1 (MQ=255)                                                                                                                aatcatcccGCCGCTATTATATCGCTCTCTTTAACCCATTCTGTTTTATCGATTCTAATTCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTAGTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCtt                                                                                                                       <  2:55128/243‑1 (MQ=255)                                                                                                                         gccgcTATTATATCGCTCTCTTTAACCCATTCTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGAtt                                                                                                            >  2:41290/1‑251 (MQ=255)                                                                                                                               attctatCGCACTCTTTAACCCCACCTGCTTTATCGCTTCTAATCCTGAAGCAGCCTCGCATTTTTCTAGCGTAATTTTTTACTGATTTAATTATTTAACTTTATTTTCTCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTATTGCAATATTGTCCTAACTAGTAAAGCCCACTGACAAGAATTTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCtgg                                                                                                      >  2:63286/5‑249 (MQ=255)                                                                                                                                 tataTCGCTCTCTTTAACCCATTCTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCtggg                                                                                                     <  2:480018/250‑4 (MQ=255)                                                                                                                                               tAACCCATTCTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACttt                                                                                                                                                      >  1:340888/1‑187 (MQ=255)                                                                                                                                               tAACCCATTCTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACttt                                                                                                                                                      <  2:340888/187‑1 (MQ=255)                                                                                                                                               tAACCCATTCTGTTTTATCGATTCTAATCCTGAAAACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCg                                                                                       <  2:484162/250‑1 (MQ=255)                                                                                                                                                                        aaTCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGcc                                                                        >  1:426846/1‑240 (MQ=255)                                                                                                                                                                        aaTCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGcc                                                                        <  2:426846/240‑1 (MQ=255)                                                                                                                                                                         aTCCTGAAGACGGCTCGCATTTTTGTGGCGTCATTTTTTATTGATTTAATTATTTAACTTTAATTTATCTATCTATAGCAATTATTGCCGACAAGCTGGATTATTTTTGAACTATTGCCCTAACAAATAACGCAGACTGACAAGACATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATATGAGCTTCGGCTCTCTCGTGAGCGCTTACAGCCGTCaaatacctc                                                            >  2:329045/1‑245 (MQ=255)                                                                                                                                                                               aaGACGCCTCGCATTTTTGTGGAGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCaaaaaactcatctc                                                       >  2:428952/1‑241 (MQ=255)                                                                                                                                                                                     ccTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTgacgac                                                                                                                                                                                                                           <  2:591855/80‑1 (MQ=255)                                                                                                                                                                                     ccTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTgacgac                                                                                                                                                                                                                           >  1:591855/1‑80 (MQ=255)                                                                                                                                                                                     ccTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTGTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCGCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGGCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTg                                                <  1:269619/251‑1 (MQ=255)                                                                                                                                                                                           aTTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGTattatt                                                                                                                                                                                                              <  2:422479/87‑1 (MQ=255)                                                                                                                                                                                           aTTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGattatt                                                                                                                                                                                                              >  1:422479/1‑87 (MQ=255)                                                                                                                                                                                                tgtgGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTCTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAAt                                     >  2:613947/1‑251 (MQ=255)                                                                                                                                                                                                 gtgGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAATTATTGTCCTAACAAATAACGCCGCCTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTAACCTTAAGCTATGATTTTCTGTGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCACTGATGGCGCAAAtt                                    >  2:380938/1‑251 (MQ=255)                                                                                                                                                                                                         aTTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAAtg                            >  1:119527/1‑250 (MQ=255)                                                                                                                                                                                                         aTTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAAtg                            <  2:209526/251‑2 (MQ=255)                                                                                                                                                                                                           tttttAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGAt                                                                                                             >  1:537463/1‑168 (MQ=255)                                                                                                                                                                                                           tttttAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGAt                                                                                                             <  2:537463/168‑1 (MQ=255)                                                                                                                                                                                                               tAATGATTTAATTATTTAACTTTAATTTATCTCTTTATCGAAATTATTGAAGACAATCTGGTTTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAATAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAATCTATGATTATCTGTGATTAGGGTCACTCGTGCACGCTTACAGCTGTCAAAAAACTCTTCTCACCGCTGATGTCGCCATTTCTTCAAtggatcgt                      >  2:356044/1‑244 (MQ=255)                                                                                                                                                                                                                      ttAATTATTTAACTTTAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTTAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCATAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTAATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTaaaaaa                <  2:388717/250‑1 (MQ=255)                                                                                                                                                                                                                                    ttAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCt                                                 <  2:219522/203‑1 (MQ=255)                                                                                                                                                                                                                                    ttAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCt                                                 >  1:219522/1‑203 (MQ=255)                                                                                                                                                                                                                                    ttAATTTATCTCTTTATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGTCCTAACAAATAACGCCGACTGACAAGAAATTAATTATTACTTTTCCTAATTAATCCCTCAGAAATCCTCACCTTAAGCTATGATTATCTGGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAAACTCATCTCACCGCTGATGGCGCAAATTCTTCAATGGATCGTAAAAAACGAGTTATTCCTac  <  2:254263/250‑1 (MQ=255)                                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                            AAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTGACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAATTATTACTTTTCCTAATTAATCCCTCAGGAATCCTCACCTTAAGCTATGATTATCTAGGCTTAGGGTCACTCGTGAGCGCTTACAGCCGTCAAAAA‑CGCATCTCACCGCTGATGGCGCAAATTCTTCAATAGCTCGTAAAAAACGAATTATTCCTAC  >  NC_000913/16934‑17409

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑