Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,756,045	T→C	intergenic (+90/‑114)	ssrA → / → intA	tmRNA/integrase IntA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,756,045	0	T	C	96.2%	80.4 / NA	26	intergenic (+90/‑114)	ssrA/intA	tmRNA/integrase IntA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (14/11);  minor base A (1/0);  total (15/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01

CTGGGGTTGAAGCGTTAAAACTTAATCAGGCTAGTTTGTTAGTGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTT‑TACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAAACCTAAAGATGCCGATTACCAGCTTTATGACGGTGACGGGCTTACTCTGTTAATCAAGTCC  >  NC_000913/2755807‑2756269                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                  cgggggTTGAAGCGTTAAAACTTAATCAGGCTAGTTTGTTAGGGGCGTGTCGGTCCGCAGCTGGCAAGCGAATGTAAAGTCTGTCTAAGCATGTAGGACCGAGTATTGAGGAATTTCGGACGGGGGTTCGACTCCCGCCAGCGCCACCAAAATGCTCCATCTGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGTTGCTGGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGaa                                                                                                                                                                                                                       <  1:594846/249‑1 (MQ=255)      gTTGAAGCGTTAAAACTTAATCAGGCTAGTTTGTTAGTGGCGTGTCCGTCCGCAGCTTGCAAGCGGATGTAAAAACTGACTAAGCCTGTAGTACCGAGGGTGTTGGAATTTCTGGCGCGGGGGCAACTCCCGCCCACTCCCCCAAAATTCTCCCTAGGGGATTTCCAAAGTCATCCGCCGAAGTCCTAAGAGCCCGCCCGGCGCAAGCCCCGCGGGCTTTTTTTTGGCCTCCACTCGTTCCGCTAAGTCCg                                                                                                                                                                                                                  >  2:159999/1‑251 (MQ=255)                    ccTTAATCGGGCTAGTTTGTTAGGGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACGGACTAAGCATGTAGTACCGAGGAGGTAGGAATTTCGGACGCGGGTTCAACCCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTa                                                                                                                                                                                                    <  2:142351/250‑1 (MQ=255)                          acagggtattttGTTAGTGGCGTGCCCGTCCTGTGCTGGCAGGGGAATGTAAAGACTGACGAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACCCCCGCCAGCTCCACCAAAATTCTCCATCGGGTATTACCAGAGTCATCCGAGGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTGTGTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGATAACTAATTAAATCCg                                                                                                                                                                                              <  2:596492/242‑1 (MQ=255)                            atgCTAGTTTTTTGGTGGCGTGGCCGTCGGCATTTGGCAAGCGAATGTAAAGTCTGACTAAGCATGTATTACCGAGGAGGTGGGAATTTCGGACGCGGGTTGAACTCCCGCCAGCTCCACCAAAATGCTCCATCGGTGATTACCAGAGGCATCCGATGAAGGCCGAAGAGCCCGCACAACTCAAGCCCTGCGGGCTTGTTGGTGCCCTCAACGCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGaa                                                                                                                                                                                            <  1:565124/249‑1 (MQ=255)                                    ttGTTAGTGGCGTGTCCGTCCGAAGCAGGCAAGCGAATGTAAAGCCTGACTAAGCATGTAGTACCGAGGATGTAGGAATTGCGGACGCGGGTCAAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCTAAGAGAACTAATTAAAGCCGAACCTTTTa                                                                                                                                                                                     <  1:196675/250‑1 (MQ=255)                                     tGTTAGTGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAg                                                                                                                                                                                    <  1:111219/250‑1 (MQ=255)                                            ggCGTGTCCGTCAGCAGCTGGAAAGCGAATGTAAAGTCTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGAGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGAGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGACCGAAGAGAACTACTTAAATCCGAACCTTTTAGTCCCATTg                                                                                                                                                                            >  2:207025/1‑251 (MQ=255)                                                          cAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGCTGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGCAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGa                                                                                                                                                               >  1:222901/1‑250 (MQ=255)                                                           aGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGaaa                                                                                                                                                             <  1:485110/251‑1 (MQ=255)                                                              tGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTaa                                                                                                                                                                                                       >  1:440055/1‑206 (MQ=255)                                                                                                           gTAGGAATTCCGGACGCGTGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTT‑TACGTTGGGCCTAAACGCAGGGAGACTCCCCATgg                                                                                                             <  2:118764/250‑1 (MQ=255)                                                                                                                    tagaacgggggTTCACCCCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTT‑TACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGaaaaa                                                                                                    <  2:12876/242‑1 (MQ=255)                                                                                                                            gggTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTT‑TACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGt                                                                                           >  1:344751/1‑251 (MQ=255)                                                                                                                                        ggCCAGCTCCAACAACATTATCCATCGGCGATTACCAGAGTCATCCGATGAAGTACTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAAATCGTCCCGCGAAGTCCGAAGAGCACTACTTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTT‑TATGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAACACCAAGCCGTTAACTGATACgg                                                                               >  2:394435/2‑251 (MQ=255)                                                                                                                                                  accaAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTT‑TACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAgc                                                                     <  1:209136/251‑1 (MQ=255)                                                                                                                                                                 cGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTT‑TACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAAACCTaa                                                         >  1:61067/1‑248 (MQ=255)                                                                                                                                                                         aCCAGAGTCGTCCGATGAAGTCCTAAGAGCCCGACCGCCGCAAGCCCTGAGGGCTTTTTGGGCCCCTCAACTCTACCCTCTAAGTCCAAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTAAGAGGCCCAACGAAAAGCGCTAT‑GTTCGACTTTGGGCCTAAACGCAGGGAGACGCCCCATGACAAGAAAATCCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAATCCTAAAGATGCCGAtt                                              <  2:410314/251‑1 (MQ=255)                                                                                                                                                                                  aTCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTT‑TACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAATCCGCCAAACCTAAAGATGCCGATTACCAGCttt                                     >  1:263355/1‑251 (MQ=255)                                                                                                                                                                                         gAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTCAGACCTCAACTCGTCCCGCGAAGTCCCAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAAGCCCAACCAAAAGCTCTATTGTT‑TACGATGGGCCTAAACACCGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGACATCAAAGCCGCCACACCTAAAGATGCCGATTACCCGCTTTAtgccgg                              >  1:593612/1‑251 (MQ=255)                                                                                                                                                                                          aaGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTT‑TACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAAACCTAAAGATGCCGATTACCAGCTTTAtgacggg                             >  1:16703/1‑250 (MQ=255)                                                                                                                                                                                                 aaGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTT‑TACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAACCGCCAAACCTAAAGATGCCGATTACCAGCTTTATGACGGTGACGGGc                      >  2:437912/1‑251 (MQ=255)                                                                                                                                                                                                     gCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTACATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTT‑TACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATCCGGAAATCAAAGCCGCCAAACCTAAAGATGCCGATTACCAGCTTTATGACGGTGACGGGCTTAc                  >  2:538486/1‑251 (MQ=255)                                                                                                                                                                                                       ccGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTT‑TACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAAACCTAAAGATGCCGATTACCAGCTTTATGACGGTGACGGGCTTActc                >  1:317049/1‑251 (MQ=255)                                                                                                                                                                                                         gCACGGCGCAAGCCCTGCGGGCTTTTTTGGGACCTCAACTCGTCCCGCGAAGTACGAAGAGGACTAATTAAATCCGAGCCGTTTAGGCCCATTGATAGGCACAACGAAAAGCACTATTGTT‑TACGTTGAGCCTAAACGCAGGGAGACCCCCAATGGCAAGAAAACCCAAGCCGTAAACTGATACGGAAATCAAAGCCGCCGAACCTACAAAAGCCGATTACCGGCTTTATGACGGTGGCGAGCTTActctt              >  1:322428/1‑250 (MQ=255)                                                                                                                                                                                                                      ccTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTT‑TACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAAACCTAAAGATGCCGATTACCAGCTTTATGACGGTGACGGGCTTACTCTGTTAATCAAGTcc  >  1:553316/1‑250 (MQ=255)                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                  CTGGGGTTGAAGCGTTAAAACTTAATCAGGCTAGTTTGTTAGTGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTT‑TACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAAACCTAAAGATGCCGATTACCAGCTTTATGACGGTGACGGGCTTACTCTGTTAATCAAGTCC  >  NC_000913/2755807‑2756269

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑