Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,808,224	A→C	noncoding (15/73 nt)	rirA ←	small regulatory RNA RirA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,808,224	0	A	C	100.0%	111.1 / NA	31	noncoding (15/73 nt)	rirA	small regulatory RNA RirA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (11/20);  total (11/20)

CCCGCACCTTTATTGCTTATCCCATAGAGCGCATTAATTTCCGGGTTTTCAGACAAAATAGGGATGGTGTCCTGATAAAGCAGCATATCGATTTTTGCATCAGGATAATTCTGCTTGAGCGTACTGATGACAGGAGTAGTTAATAACATATCCCCATGATATCGCATCTTTATGACCAGGATTTTTCGAAATGGCTTTTCCACTAGCGACTCTTTT‑GT‑GT‑GATTGTCTGGTTAAG‑TTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGCTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATGATTTTTATACACAAAATATACTTTA  >  NC_000913/3807932‑3808306                                                                                                                                                                                                                                                                                                         |                                                                                   ttttcttttttattttttatgccgtAGAGCGCTTTAATCTCTGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAATCAGCACATCGNTTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCac                                                                               <  2:546744/276‑1 (MQ=255)      ttttttattttttatgccgtAGAGCGCGTTAATCTCTGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCactgata                                                                          <  1:279091/281‑5 (MQ=255)       tttttattttttatgccttAGAGCGCGTTAATCTCTGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCactgatat                                                                         <  1:703081/282‑6 (MQ=255)       tttttattttttatgccgtAGAGCGCGTTAATCTCTGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCactgatat                                                                         <  1:430736/282‑6 (MQ=255)       tttttattttttatgccgtAGAGCGCGGTAATCTCTGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCactgatat                                                                         <  2:145659/282‑6 (MQ=255)         tttattttttatgccgtAGAGCGCGTTAATCTCTGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCactgatattg                                                                       <  1:107323/284‑8 (MQ=255)         tttattttttatgccgtAGAGCGCGTTAATCTCTGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCactgatatt                                                                        >  2:664272/17‑293 (MQ=255)          ttattttttatgccgtAGAGCGCGTTAATCTCGGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCGTGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTTAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCactgatattga                                                                      <  2:167420/285‑9 (MQ=255)           tattttttatgccgtAGAGCGCGTTAATCTCTGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCactgatattgac                                                                     <  1:72533/286‑10 (MQ=255)           tattttttatgccgtAGAGCGCGTTAATCTCTGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGT‑TTAGATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCactgatattgac                                                                     <  1:280959/286‑10 (MQ=255)            attttttatgccgtAGAGCGCGTTAGTCTCTGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTGTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAAGTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAGAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCactgatattg                                                                       <  2:76601/284‑8 (MQ=255)                     gccgtAGAGCGCGTTAATCTCTGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAgtgt                                                           >  1:26913/5‑300 (MQ=255)                     gccgtAGAGCGCGTTAAGCTCTGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAgtgt                                                           <  2:411117/296‑1 (MQ=255)                        gtAGAGCGCGTTAATCTCTGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTNAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAGTGTAt                                                         <  1:134566/298‑1 (MQ=255)                        gtAGAGCGCGTTAATCTCTGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAGTGTAt                                                         <  1:286701/298‑1 (MQ=255)                         tAGAGCGCGTTAATCTCTGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAGTGTATCa                                                       <  1:219784/300‑1 (MQ=255)                         tAGAGCGCGTTAATCTCTGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTNTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGT‑TTAGATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAGTGTAt                                                         <  2:553618/298‑1 (MQ=255)                          agagCGCGTTAATCTCTGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAGTGTATCac                                                      <  1:177070/300‑2 (MQ=255)                          agaacgcgttaatctctggattttCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAGTGTATCac                                                      <  1:264301/280‑2 (MQ=255)                            agCGCGTTAATCTCTGGATTTTCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAGTGTATCactt                                                    <  1:119403/300‑4 (MQ=255)                                ctgcgagatgtgtataagagacagggatcgggATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGATTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAGTGTATCActtcttt                                                >  1:197493/30‑300 (MQ=255)                                           ggattttCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAGTGTATCACTTCTTTCGCGGCAATcc                                     <  1:107531/297‑1 (MQ=255)                                           ggattttCAGACAGGATCGGGATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGT‑TTAGATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAGTGTATCACTTCTTTCGCGGCAATcc                                     <  1:108153/297‑1 (MQ=255)                                                        ggatcgggATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAGTGTATCACTTCTTTCGCGGCAATCCGGCCCGAATGAtt                        >  2:466794/6‑300 (MQ=255)                                                        ggatcgggATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAGTGTATCACTTCTTTCGCGGCAATCCGACCCGAATGAtt                        >  1:194819/6‑300 (MQ=255)                                                        ggatcgggATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAGTGTATCAATTCTTTCGCGGCAATCCGACCCGAATGAtt                        >  2:570094/6‑300 (MQ=255)                                                           tcgggATGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAGTGTATCACTTCTTTCGCGGCAATCCGACCCGAATGAttttt                     >  1:520750/3‑300 (MQ=255)                                                                aTGGTGTCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAGTGTATCACTTCTTTCGCGGCAATTCGACCCGAATGATTTTtaagca                >  1:265888/1‑296 (MQ=255)                                                                    tgtCCTGATAAAGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAGTGTATCACTTCTTTCGCGGCAATCCGACCCGAATGATTTTtaagcacatt            >  2:472717/1‑292 (MQ=255)                                                                              aaGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAGTGTATCACTTCTTTCGCGGCAATCCGACCCGAATGATTTTtaagcacattgttgattttc  >  1:364588/1‑282 (MQ=255)                                                                              aaGCAGCACATCGATTTTTGCGTCAGGGTAATTTTTTTTCAGCGAACTAATGACGGGAGTAGTTAATAACATATCCCCATGAAAACGCATCTTAATGAGCAAAATTCTTCGAAATGGCTTATCCACAAGTAACTCTTTTTGTTGA‑GATTATCCGATTAAGGTGAAGCAGAAAAA‑GCACGTTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATACCGCACTGATATTGACGCGCTAGTGTATCACTTCTTTCGCGGCAATCCGACCCGAATGATTTTtaagcacattgttgattttc  >  2:604244/1‑282 (MQ=255)                                                                                                                                                                                                                                                                                                         |                                                                                   CCCGCACCTTTATTGCTTATCCCATAGAGCGCATTAATTTCCGGGTTTTCAGACAAAATAGGGATGGTGTCCTGATAAAGCAGCATATCGATTTTTGCATCAGGATAATTCTGCTTGAGCGTACTGATGACAGGAGTAGTTAATAACATATCCCCATGATATCGCATCTTTATGACCAGGATTTTTCGAAATGGCTTTTCCACTAGCGACTCTTTT‑GT‑GT‑GATTGTCTGGTTAAG‑TTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGCTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATGATTTTTATACACAAAATATACTTTA  >  NC_000913/3807932‑3808306

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑