Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,755,958	Δ1 bp	intergenic (+3/‑201)	ssrA → / → intA	tmRNA/CP4‑57 prophage; integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,755,955	0	A	.	100.0%	165.7 / NA	40	noncoding (363/363 nt)	ssrA	tmRNA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (19/21);  total (19/21)

AAGCGTTAAAACTTAATCAGGCTAGTTTGTTAGTGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGA  >  NC_000913/2755816‑2756083                                                                                                                                            |                                                                                                                                 aaGCGTTAAAACTTAATCAGGCTAGTTTGTTAGTGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGGTCAACTCCCGCCAGCTccacca                                                                                                                                  >  1:343931/1‑140 (MQ=255)  aGCGTTAAAACTTAATCAGGCTAGTTTGTTAGTGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCaa                                                                                                                                 >  2:1158910/1‑140 (MQ=255)      ttAAAACTTAATCAGGCTAGTTTGTTAGTGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGGTCAACTCCCGCCAGCTCCACCAAAAtt                                                                                                                             >  2:1185298/1‑140 (MQ=255)       tAAAACTTAATCAGGCTAGTTTGTTAGTGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCaaattct                                                                                                                            <  2:507027/140‑5 (MQ=255)           aCTTAATCAGGCTAGTTTGTTAGTGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCAt                                                                                                                       <  1:200041/140‑1 (MQ=255)               aaTCAGGCTAGTTTGTTAGTGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGt                                                                                                                   <  2:458555/140‑1 (MQ=255)               aaTCAGGCTAGTTTGTTAGTGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGt                                                                                                                   <  2:641185/140‑1 (MQ=255)                aTCAGGCTAGTTTGTTAGTGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTg                                                                                                                  <  1:912458/140‑1 (MQ=255)                                   ggCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGGATTTCGGACGCGGGGTCAACTCCCGCCAGCTCCACCAAAA‑TCTCCATCGGGGATTACCCGAGTCATCCGAt                                                                                               >  2:261186/1‑140 (MQ=255)                                   ggCGTGGCCGGCCGCAGCCGGCAAACGCATTGAAAAAACGACTAAGCATTGAGTACCGGGGATGTAGGGATTTCGGGCGCGGGGTCAACTCCCGCCAGCTCCACC‑AAATTCTTCATCAGGGGTTACCACAGTCATCCGaa                                                                                               >  2:237235/1‑139 (MQ=255)                                     cGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGa                                                                                             <  2:892079/140‑1 (MQ=255)                                       tgtCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAg                                                                                           <  2:658092/140‑1 (MQ=255)                                       tgtCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGGTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAg                                                                                           >  1:20540/1‑140 (MQ=255)                                         tccgtccgCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTc                                                                                         >  1:11966/1‑140 (MQ=255)                                           cgtccgCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCt                                                                                       <  2:164345/140‑1 (MQ=255)                                                      ggCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCa                                                                            <  1:224817/140‑1 (MQ=255)                                                      ggCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCa                                                                            <  1:237235/140‑1 (MQ=255)                                                      ggCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCa                                                                            <  1:38442/140‑1 (MQ=255)                                                         aaGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACgg                                                                         >  2:115036/1‑140 (MQ=255)                                                           gCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGgcg                                                                       <  2:1149274/140‑1 (MQ=255)                                                                         tgactAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGc                                                         >  1:1127705/1‑140 (MQ=255)                                                                          gactAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCt                                                        >  2:847791/1‑140 (MQ=255)                                                                          gactAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCt                                                        >  2:915233/1‑140 (MQ=255)                                                                               aGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCtttttt                                                   <  1:261186/140‑1 (MQ=255)                                                                                 cATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTtgt                                                 <  1:915233/140‑1 (MQ=255)                                                                                 cATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTtgt                                                 >  1:256802/1‑140 (MQ=255)                                                                                  aTGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTtgtg                                                <  2:11966/140‑1 (MQ=255)                                                                                     tagtaCCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGccc                                             >  2:1176511/1‑140 (MQ=255)                                                                                     tagtaCCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGccc                                             >  1:1210564/1‑140 (MQ=255)                                                                                         aCCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCaa                                         <  1:1185298/140‑1 (MQ=255)                                                                                          ccGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAAt                                        <  2:256802/140‑1 (MQ=255)                                                                                          ccGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAAt                                        <  1:1176511/140‑1 (MQ=255)                                                                                          ccGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAAt                                        <  2:1210564/140‑1 (MQ=255)                                                                                             aGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTg                                     >  2:204237/1‑140 (MQ=255)                                                                                             aGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTg                                     >  1:313418/1‑140 (MQ=255)                                                                                             aGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTg                                     >  2:1147272/1‑140 (MQ=255)                                                                                               gATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTc                                   >  2:466072/1‑140 (MQ=255)                                                                                               gATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTc                                   >  2:839189/1‑140 (MQ=255)                                                                                                   tAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCcgc                               >  2:19538/1‑140 (MQ=255)                                                                                                    aGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCcgcg                              <  1:839189/140‑1 (MQ=255)                                                                                                         tttCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTc                         >  1:187568/1‑140 (MQ=255)                                                                                                         tttCGGACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCAAAGTc                         >  1:1166832/1‑140 (MQ=255)                                                                                                             ggACGCGGGTTCAACTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGaa                     <  1:1158910/140‑1 (MQ=255)                                                                                                                           cTCCCGCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTaaa       >  2:783103/1‑140 (MQ=255)                                                                                                                                gCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGa  <  2:187568/140‑1 (MQ=255)                                                                                                                                gCCAGCTCCACC‑AAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGa  >  2:1192583/1‑140 (MQ=255)                                                                                                                                            |                                                                                                                                 AAGCGTTAAAACTTAATCAGGCTAGTTTGTTAGTGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGA  >  NC_000913/2755816‑2756083

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑