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	100.0%	77.4 / NA	25	intergenic (+90/‑114)	ssrA/intA	tmRNA/integrase IntA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (13/12);  total (13/12)

GTTGAAGCGTTAAAACTTAATCAGGCTAGTTTGTTAGTGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAAACCTAAAGATGCCGATTACCAGCTTTATGACGGTGACGGGCTTACTCTGTTAATCAAGTCCAGTGGCAGT  >  NC_000913/2755812‑2756278                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                          gTTGAAGCGTTAAAACTTAATCAGGCTAGTTTGTTAGTGGCGTATCCGTCCGCAGCTGGCAAAAGAATGTAAAGACTGACTAAGCATGTAGGACCGCGGGTGTAGGAATTTCGGACCCGGGTTCCAATCCCGCCAGCCCCACCCAAATTCTCCCTCGGTGATTACCCAAGTCATTCGATGAAGGCCTAAGAACCCCCACGGCGCAAGGCCAGCGGGCTTTTTTGTGCCCTCAACTCGTCCCCCGAAGTCCg                                                                                                                                                                                                                          >  1:59035/1‑251 (MQ=255)    gaagcatgaaaccTTAATCAGTGTAGTTTGTTAGGGGCTGGTCCGTCCGGAGCTGTCGAGGGAAGGTAAGGTCTGACTAAGTATGTATTGGGGAGAATGGGGGAATTGCGGACGCGGGTTCAACTCCCGCCAGCGCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATGCGATGGAGTCCGAAGAGCCCGCACGGCGCAAGCGCTGCGGGGGTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAag                                                                                                                                                                                                                       <  1:292485/239‑1 (MQ=255)                                   tAGTGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTCCCGAGGAGGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGTCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGcc                                                                                                                                                                                         <  1:483073/250‑1 (MQ=255)                                          gtgtCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGAt                                                                                                                                                                                  >  1:461073/1‑250 (MQ=255)                                                          ggCAAGGGAATGTAAAGAATGCCGAAGCAGGTAGTCCCGAGGATGTAGGAATTCCGGCCGCGGGTTCAACTCCCGCCAGCTCCACCAAAATGCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGct                                                                                                                                                                 <  2:414497/251‑1 (MQ=255)                                                             aaGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAg                                                                                                                                                                                                                              <  1:93498/187‑1 (MQ=255)                                                             aaGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAg                                                                                                                                                                                                                              >  2:93498/1‑187 (MQ=255)                                                                 gAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAAAGAAAAGCTCTATTGt                                                                                                                                                          >  1:372025/1‑251 (MQ=255)                                                                   aTGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGttt                                                                                                                                                        >  1:55909/1‑251 (MQ=255)                                                                            ctgactAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                                                                                                                               >  1:69592/1‑251 (MQ=255)                                                                                                   gagttAGGAATTTCGGACGGGGTTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCGGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAAGTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGTAGGGAGACTCCCCAt                                                                                                                        <  2:414262/247‑1 (MQ=255)                                                                                                                gggACGCGGATTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAAcc                                                                                                           <  2:372025/250‑1 (MQ=255)                                                                                                                           tcaccccccGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCGGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCAAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTaa                                                                                                 <  2:55909/244‑1 (MQ=255)                                                                                                                            cAACTCCCGACAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGACAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACt                                                                                               >  2:41257/1‑251 (MQ=255)                                                                                                                              aCTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTg                                                                                              >  1:212609/1‑250 (MQ=255)                                                                                                                                           ccaccaAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACGCGTCCCGCGAAGTCCGAAGAGAACTAAGTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCGATTGTTTACGTTGGGCCTAAACGCAGGGAGACACCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCaaa                                                                                <  2:74884/251‑1 (MQ=255)                                                                                                                                             accaAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAgc                                                                              >  2:88705/1‑251 (MQ=255)                                                                                                                                                 aaaTTCTCCATCGGTGATTCCCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACTGAAATCAAAgccgcc                                                                          <  1:355560/251‑1 (MQ=255)                                                                                                                                                                  ttACCAGAGTCATCCGCTGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAAACCTAAAGATGCCg                                                          >  2:35331/1‑250 (MQ=255)                                                                                                                                                                             ccccGAAGAAGGCCTAAGAGCCCGCACGGCGCAAGCCGTGCGGGCTTTTTTGTGCCCCCAACTCGACCCGCGAAGTCCGAAGAGAACTAATTAAACCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAAAAAAACCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAAACCTAAAGAGGCCGATTGCCAGCttt                                              <  2:46674/249‑1 (MQ=255)                                                                                                                                                                                  aTGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAAACCTAAAGATGCCGATTACCAGCTTTAtgac                                         >  1:13099/1‑251 (MQ=255)                                                                                                                                                                                                    gCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAAACCTAAAGATGCCGATTACCAGCTTTATGACGGTGACGGGCTTACTCTg                       <  2:212609/251‑1 (MQ=255)                                                                                                                                                                                                             aaGCCCTGCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAAACCTAAAGATGCCGATTACCAGCTTTATGACGGTGACGGGCTTACTCTGTTAATCa                >  1:353227/1‑249 (MQ=255)                                                                                                                                                                                                                    gCGGGCTTTTTTGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAAACCTAAAGATGCCGATTACCAGCTTTATGACGGTGACGGGCTTACTCTGTTAATCAAGTCCAGt        <  1:88705/250‑1 (MQ=255)                                                                                                                                                                                                                          ttttttGTGCCCTCAACTCGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAAACCTAAAGATGCCGATTACCAGCTTTATGACGGTGACGGGCTTACTCTGTTAATCAAGTCCAGTGGCAGt  >  2:162361/1‑250 (MQ=255)                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                          GTTGAAGCGTTAAAACTTAATCAGGCTAGTTTGTTAGTGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAAACCTAAAGATGCCGATTACCAGCTTTATGACGGTGACGGGCTTACTCTGTTAATCAAGTCCAGTGGCAGT  >  NC_000913/2755812‑2756278

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑