Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,808,243	C→T	intergenic (‑5/‑297)	rirA ← / → waaA	small regulatory RNA RirA/KDO transferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,808,243	0	C	T	100.0%	86.6 / NA	24	intergenic (‑5/‑297)	rirA/waaA	small regulatory RNA RirA/KDO transferase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (9/15);  total (9/15)

TGTCCTGATAAAGCAGCATATCGATTTTTGCATCAGGATAATTCTGCTTGAGCGTACTGATGACAGGAGTAGTTAATAACATATCCCCATGATATCGCATCTTTATGACCAGGATTTTTCGAAATGGCTTTTCCACTAGCGACTCTTTTGTGTGATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGCTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATGATTTTTATACACAAAATATACTTTAATCATAAAAATCAAATAGATAAAAAATAGCATTTCGATAATGTCAGTACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATACAAAAAAAATGAAGATGTAGCGGCAGATCA  >  NC_000913/3807999‑3808438                                                                                                                                                                                                                                                     |                                                                                                                                                                                                    tgtCCTGATAAAGCAGCATATCGATTTTTGCATCAGGATAATTCTGCTTGAGCGTACTGATGACAGGAGTAGTTAATAACATATCCCCATGATATCGCATCTTTATGACCAGGATTTTTCGAAATGGCTTTTCCACTAGCGACTCTTTTGTGTGATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGACTACTGATAACGCACTTACTTTGACGTGTTAgtgt                                                                                                                                                                                               >  2:228424/1‑251 (MQ=255)     cTGATAAAGCAGCATATCGATTTTTGCATCAGGATAATTCTGCTTGAGCGTACTGATGACAGGAGTAGTTAATAACATATCCCCATGATATCGCATCTTTATGACCAGGATTTTTCGAAATGGCTTTTCCACTAGCGACTCTTTTGTGTGATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTATc                                                                                                                                                                                            >  2:224040/1‑250 (MQ=255)              cagcaTATCGATTTTTGCATCAGGATAATTCTGCTTGAGCGTACTGATGACAGGAGTAGTTAATAACATATCCCCATGATATCGCATCTTTATTACCAGGATTTTTCGAAATGGCTTTTCCACTAGCGACTCTTTTGTGTGATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTATCATTTCTTTCg                                                                                                                                                                                  <  1:403914/251‑1 (MQ=255)              cagcaTATCGATTTTTGCATCAGGATAATTCTGCTTGAGCGTACTGATGACAGGAGTAGTTAATAACATATCCCCATGATATCGCATCTTTATGACCAGGATTTTTCGAAATGGCTTTTCCACTAGCGACTCTTTTGTGTGATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTATCATTTCTTTCg                                                                                                                                                                                  >  1:36685/1‑251 (MQ=255)                                aTCAGGATAATTCTGCTTGAGCGTACTGATGACAGGAGTAGTTAATAACATATCCCCATGATATCGCATCTTTATGACCAGGATTTTTCGAAATGGCTTTTCCACTAGCGACTCTTTTGTGTGATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAAt                                                                                                                                                                <  1:183810/251‑1 (MQ=255)                                  cAGGATAATTCTGCTTGAGCGTACTGATGACAGGAGTAGTTAATAACATATCCCCATGATATCGCATCTTTATGACCAGGATTTTTCGAAATGGCTTTTCCACTAGCGACTCTTTTGTGTGATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATg                                                                                                                                                               <  1:279464/250‑1 (MQ=255)                                      aTAATTCTGCTTGAGCGTACTGATGACAGGAGTAGTTAATAACATATCCCCATGATATCGCATCTTTATGACCAGGATTTTTCGAAATGGCTTTTCCACTAGCGACTCTTTTGTGTGATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATGAtttt                                                                                                                                                          >  2:181684/1‑251 (MQ=255)                                      aTAATTCTGCTTGAGCGTACTGATGACAGGAGTAGTTAATAACATATCCCCATGATATCGCATCTTTATGACCAGGATTTTTCGAAATGGCTTTTCCACTAGCGACTCTTTTGTGTGATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTATCATTTCTGTCGCAGCAATCCGACCCGAATGAtttt                                                                                                                                                          <  2:264641/251‑1 (MQ=255)                                                               aCAGGAGTAGTTAATAACATATCCCCATGATATCGCATCTTTACGACCAGGATTTTTCGAAATGGCCTTTACACTAGCGACTCTTTTATGTGATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGACCCCGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGTCGGGTTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATGATTTTTATACACAAAATATACTTTAAtaat                                                                                                                                 >  1:35056/1‑248 (MQ=255)                                                                                     ccccATGATATCTCATCTTTATGACCAGGATTTTTCGAAATGGCTTTTCCACTAGCGACTCTTTTGTGTGATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATGAATTTTATACACAAAATATACTTTAATCATAAAAATCAAATAGATAAAAAAt                                                                                                           <  2:271025/251‑1 (MQ=255)                                                                                               tCGCATCTTTATGACCAGGATTTTTCGAAATGGCTTTTCCACTAGCGACTCTTTTGTGTGATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATGATTTTTATACACAAAat                                                                                                                                              <  2:214448/206‑1 (MQ=255)                                                                                               tCGCATCTTTATGACCAGGATTTTTCGAAATGGCTTTTCCACTAGCGACTCTTTTGTGTGATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATGATTTTTATACACAAAat                                                                                                                                              >  1:214448/1‑206 (MQ=255)                                                                                                       ttATGACCAGGATTTTTCGAAATGGCTTTTCCACTAGCGACTCTTTTGTGTGATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATGATTTTTATACACAAAATATACTTTAATCATAAAAATCAAATAGATAAAAAATAGCATTTCGATAATg                                                                                            <  1:316696/248‑1 (MQ=255)                                                                                                           gtccatgATTGTTCAAAATGGCCTTTCCACTAGCGACACTTTTGGGTGATTGTCTGGATAAGTTAAGCAGAAAAAAGACCGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCAATTACTTAGACGTGTTAGTGTATCATTTCTTTCACAGCAATCCGACCCGAATGATTTTTATACACAAAATATACTTTAATCATAAAAAGCAAATAGATAAAAAATAGCATTTCGATAATGTCAGttc                                                                                     <  2:311736/245‑3 (MQ=255)                                                                                                                         gAAATGGCTTTTCCACTAGCGACTCTTTTGTGTGATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATGATTTTTATACACAAAATATACTTTAATCATAAAAATCAAATAGATAAAAAATAGCATTTCGATAATGTCAGTACGGCCTATGTAGAtt                                                                       >  1:329913/1‑251 (MQ=255)                                                                                                                                  tttCCACTAGCGACTCTTTTGTGTGATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATGATTTTTATACACAAAATATACTTTAATCATAAAAATCAAATAGATAAAAAATAGCATTTCGATAATGTCAGTACGGCCTATGTAGATTTGAAAATg                                                               <  1:228424/250‑1 (MQ=255)                                                                                                                                                   tttGTGTGATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATGATTTTTATACACAAAATATACTTTAATCATAAAAATCAAATAGATAAAAAATAGCATTTCGATAATGTCAGTACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATg                                               <  1:224040/249‑1 (MQ=255)                                                                                                                                                     tgtgtgATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATGATTTTTATACACAAAATATACTTTAATCATAAAAATCAAATAGATAAAAAATAGCATTTCGATAATGTCAGTACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATc                                           >  1:332729/1‑251 (MQ=255)                                                                                                                                                        gtgATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATGATTTTTATACACAAAATATACTTTAATCATAAAAATCAAATAGATAAAAAATAGCATTTCGATAATGTCAGTACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATAAATCGc                                         <  1:123840/250‑1 (MQ=255)                                                                                                                                                             tGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATGATTTTTATACACAAAATATACTTTAATCATAAAAATCAAATAGATAAAAAATAGCATTTCGATAATGTCAGTACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATaaa                                    <  2:330541/250‑1 (MQ=255)                                                                                                                                                                  ggTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTAt                                                                                                                                                                                             >  2:249978/1‑92 (MQ=255)                                                                                                                                                                  ggTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTAt                                                                                                                                                                                             <  1:249978/92‑1 (MQ=255)                                                                                                                                                                                    aaaGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATTCTGATAACGCACTTACTTTGACGTGTTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATGATTTTTATACACAAAATATACTTTAATCATAAAAATCAAATAGATAAAAAATAGCATTTCGATAATGTCAGTACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATACAAAAAAAATGAAGATGTAg            <  1:360382/251‑1 (MQ=255)                                                                                                                                                                                              aCCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGTTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATGATTTTTATACACAAAATATACTTTAATCATAAAAATCAAATAGATAAAAAATAGCATTTCGATAATGTCAGTACGGCCTATGTAGAGTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATACAAAAAAAATGAAGATGTAGCGGCAGATCa  <  2:193620/251‑1 (MQ=255)                                                                                                                                                                                                                                                     |                                                                                                                                                                                                    TGTCCTGATAAAGCAGCATATCGATTTTTGCATCAGGATAATTCTGCTTGAGCGTACTGATGACAGGAGTAGTTAATAACATATCCCCATGATATCGCATCTTTATGACCAGGATTTTTCGAAATGGCTTTTCCACTAGCGACTCTTTTGTGTGATTGTCTGGTTAAGTTAAGCAGAAAAAAGCACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACTGATAACGCACTTACTTTGACGTGCTAGTGTATCATTTCTTTCGCAGCAATCCGACCCGAATGATTTTTATACACAAAATATACTTTAATCATAAAAATCAAATAGATAAAAAATAGCATTTCGATAATGTCAGTACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATACAAAAAAAATGAAGATGTAGCGGCAGATCA  >  NC_000913/3807999‑3808438

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑