Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,290,947	C→T	Q236* (CAA→TAA)	rssB →	regulator of RpoS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,290,947	0	C	T	100.0%	68.4 / NA	27	Q236* (CAA→TAA)	rssB	regulator of RpoS
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (14/13);  total (14/13)

GAACTACAACCGCCGGTTCAGCAGGTGATTTCCCATTGCCGGGTTAATTATCGTCAATTGGTTGCCGCGGACAAACCCGGCCTGGTGCTTGATATTGCCGCACTTTCGGAAAACGATCTGGCATTTTATTGCCTTGATGTCACCCGAGCTGGACATAATGGCGTACTTGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATCAACGGTTGCCAGAGTTGGGCGCGTTATTGAAGCAGGTAAACCATTTACTTCGTCAGGCCAATCTGCCGGGGCAGTTTCCGCTATTAGTTGGCTATTATCATCGCGAACTGAAAAATCTCATTCTGGTTTCTGCGGGTCTGAATGCGACGTTAAATACCGGCGAACACCAGGTGCAAATCAGTAATGGTGTTCCGTTAGGCACTTTAGGTAACGCTTATTTGAATCAATTGA  >  NC_000913/1290716‑1291178                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                        gAACTCCAACCACCGGTTCAGCAGGTGATTTCCCATTGCCGGGTTAATTATCGTCAATTGGTTGCCGCGGACAAACCCGTCCTGGTGCTTGATATTGCCGCACTTTCGGAAAACGATCTGGCATTTTATTGCCTTGATGTCACCCGGGCTGGACATAATGGCGTACTTGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTgtg                                                                                                                                                                                                                      >  2:110225/1‑249 (MQ=255)   aCTACAACCGCCGGTTCAGCAGGTGATTTCCCATTGCCGGGTTAATTATCGTCAATTGGTTGCCGCGGACAAACCCGGCCTGGTGCTTGATATTGCCGCACTTTCGGAAAACGATCTGGCATTTTATTGCCTTGATGTCACCCGAGCTGGACATAATGGCGTACTTGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGgcg                                                                                                                                                                                                                    >  1:78635/1‑251 (MQ=255)          ccgccgGTTCAGCAGGTGATTTCCCATTGCCGGGTTAATTATCGTCAATTGGTTGCCGCGGACAAACCCGGCCTGGTGCTTGATATTGCCGCACTTTCGGAAAACGATCTGGCATTTTATTGCCTTGATGTCACCCGAGCTGGACATAATGGCGTACTTGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGGCGCGTTAtt                                                                                                                                                                                                             <  1:105005/251‑1 (MQ=255)          ccgccgGTTCAGCAGGTGATTTCCCATTGACGGGTTAATTATCGTCAATTGGTTGCCGCGGACAAACCCGGCCTGGTGCTTGATATTGCCGCACTTTCGGAAACCGATCTGGCATTTTATTGCCTTGATGTCACCCGAGCTGGACATAATGGCGTTCTTGCTTCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACCGCTTGCACACCAAAATTCACGGTTGCCAGAGTTTGGTGCGTTAtt                                                                                                                                                                                                             >  2:58894/1‑251 (MQ=255)                    agccggcgattttccgttgaggggTTAAGTATCGTGATTTGGTCGCCGCGGAAAAACCTGGCCTGGTGATTGATATTGCCGCAATTTCGGAAAACGATCTGGTATTTTAGTGCCTTGATGTTACCCGATCTGGAAATAATGGCGTACGTGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCGTGCACGTCAAAAGTAACGGTTGCCAGATTTGGTCGCGTTATTGAAGCAGGTa                                                                                                                                                                                                   <  2:347148/230‑1 (MQ=255)                       agGTTATTTCCCATTGCCTGGTTAATTATCGTCAAGTGGGTGCCGCGGACAAACCCGGCCTGGTGCTTGATAGTGCCGCACTTTCGGAAAACGCTCTGGCATTGTATTGCCTTGATGTCACCCGAGCTGGACATAATGGCGTACTTGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGGCGCGTTATTGAAGCAGGTAAAc                                                                                                                                                                                                <  2:91820/251‑1 (MQ=255)                        ggTGATTTCCCATTGCCGGGTTAATTATCGTCAATTGGTTGCCGCGGACAAACCCGGCCTGGTGCTTGATATTGCCGCACTTTCGGAAAACGATCTGGCATTTTATTGCCTTGATGTCACCCGAGCTGGACATAATGGCGTACTTGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGGCGCGTTATTGAAGCAGGTAAAcc                                                                                                                                                                                               >  1:235809/1‑251 (MQ=255)                                  cagtGCCGCGTTAATTATAGTCATTTGATTCCCGCGAACACCCACGGCCTGGTGCTTGATATTGCCTCCCTTTCGGAAAACGACCTGACCTTTTACTGCCTTGCTGTCCCCCGAGCTGGACATAATGGCGTACTTCCTGCCTTGTCATTACGCGCATTGTTTAACGGATTATTACAGGAACATATTGCATACCCAAATTCACGCATGCCAGCTTTGGGCGCGTTATTGAAGCGGGTAAACCATTTACTTCg                                                                                                                                                                                     >  2:15369/4‑251 (MQ=255)                                      gCCGGGTTAATTATCGTCAATTGGTTGCCGCGGACAAACCCGGCCTGGTGCTTGATATTGCCGCACTTTCGGAAAACGATCTGGCATTTTATTGCCTTGATGTCACCCGAGCTGGACATAATGGCGTACTTGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGGTGGGCGCGTTATTGAAGCAGGTAAACCATTTACTTCGTCAg                                                                                                                                                                                 <  2:271220/251‑1 (MQ=255)                                            ttAATTATCGTCAATTGGTTGCCGCGGACAAACCCGGCCTGGTGCTTGATATTGCCGCACTTTCGGAAAACGATCTGGCATTTTATTGCCTTGATGTCACCCGAGCTGGACATAATGGCGTACTTGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGGTGGGCGAGATATTGAAGCAGGTAAACCATTTACTTCGTCCGGCCAAt                                                                                                                                                                           >  1:335844/1‑251 (MQ=255)                                                  aTCGTCAATTGGTTGCCGCGGACAAACCCGGCCTGGTGCTTGATATTGCCGCACTTTCGGAAAACGATCTGGCATTTTATTGCCTTGATGTCACCCGAGCTGGACATAATGGCGTACTTGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGGCGCGTTATTGAAGCAGGTAAACCATTTACTTCGTCAGGCCAATCTGCCg                                                                                                                                                                     <  1:294215/251‑1 (MQ=255)                                                      gatagtgggttcagcgGTCAAACCCGGTCTGGTGCTTGATATTGCCGCACGTTCGGAAAACGACCTGGCATTTTATGGCCTTGGTGTCACCCGAGCTGGACATAATGGCGTACGTGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGTAACAGCTTGCACACCAAAATTAACGGGTGCCAGAGTTGGGCGCGGTATGGAAGCAGGTAAACCATTTACTGCGTCAGGCCAATCTGCCGGGGc                                                                                                                                                                 <  2:53878/238‑1 (MQ=255)                                                                           aCCCGGCCTGGTGCTTGATATTGCCGCACTTTCGGAAAACGATCTGGCATTTTATTGCCTTGATGTCACCCGAGCTGGACATAATGGCGTACTTGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGGCGCGTTATTGAAGCAGGTAAACCATTTACTTCGTCAGGCCAATCTGCCGGGGCAGTTTCCGCTATTAGTTGGCt                                                                                                                                            <  2:78635/251‑1 (MQ=255)                                                                           aCCCGGCCTGGTGCTTGATATTGCCGCACTTTCGGAAAACGATCTGGCATTTTATTGCCTTGATGTCACCCGAGCTGGACATAATGGCGTACTTGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGGCGCGTTATTGAAGCAGGTAAACCAGTTACTTCGTCAGGCCAATCTGCCGGGGCAGTTTCCGCTATTAGTTGGCt                                                                                                                                            <  2:192639/251‑1 (MQ=255)                                                                                         ttGATATTGCCGCACTTTCGGAAAACGATCTGGCATTTTATTGCCTTGATATCACCCGAGCTGGACATAATGGCGTACTTGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGGCGCGTTATTGAAGCAGGTAAACCATTTACTTCGTCAGGCCAATCTGCCGGGGCAGTTTCCGCTATTAGTTGGCTATTATCATCGCGa                                                                                                                               >  1:3606/1‑250 (MQ=255)                                                                                                  ccGCACTTTCGGAAAACGATCTGGCATTTTATTTCCTTGATGTCACCCGAGCTGGACATAATGGCGTACTTGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGGCGCGTTATTGACGCAGGCAAACCCTTTACTTCGTCAGGCCAATCTGCCGGGGCAGTTTCCGCTATTAGTTGTCTATTATCATCGAGAACTGAAAAAt                                                                                                                     >  1:172933/1‑251 (MQ=255)                                                                                                                aaCGATCTGGCATTTTATTGCCTTGATGTCACCCGAGCTGGACATAATGGCGTACTTGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGGCGCGTTATTGAAGCAGGTAAACCATTTACTTCGTCAGGCCAATCTGCCGGGGCAGTTTCCGCTATTAGTTGGCTATTATCATCGCGAACTGAAAAATCTCATTCTGGTTTc                                                                                                       >  1:9780/1‑251 (MQ=255)                                                                                                                        ggCATTTTATTGCCTTGATGTCCCCCGAGCTGGACATAATGGCGTACTTGCTGCCTTGTTATTACGCTCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGGCGCGTTATTGAAGCAGGTAAACCATTTACTTCGTCAGGCCAATCTTCCGGGGCAGTTTCCGCTATTAGTTGGCTATTATCATCGCGAACTGAAAAATCTCATTCTGGTTTCTGCg                                                                                                   <  2:235809/247‑1 (MQ=255)                                                                                                                                        gATGTCACACGAGCTGGACATCATGGCGTACTTGCTGCCTTGTTATTACGCGCCTTGTTTAACGGATTATTACAGGAACCGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGGCGCGTTATTGCAGCAGGTAAACCATTTACTTCGTCAGGCCAATCTGCCGGGGCAGTTTCCGCTATTAGTTGGCTATTATCATCGCGAACTGAAAAATCTCATTCTGGTTTCTGCGGGTCTGCATGCGACGTTaa                                                                                >  2:24242/1‑250 (MQ=255)                                                                                                                                                           aTAATGGCGTACTGGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGGCGCGTTATTGAAGCAGGTAAACCATTTACTTCGTCAGGCCAATCTGCCGGGGCAGTTTCCGCTATTAGTTGGCTATTATCATCGCGAACTGAAAAATCTCATTCTGGTTTCTGCGGGTCTGAATGCGACGTTAAATACCGGCGAACACCAGGTg                                                            <  2:3606/251‑1 (MQ=255)                                                                                                                                                            tAATGGCGTACTTGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGGCGCGTTATTGAAGCAGGTAAACCATTTACTTCGTCAGGCCAATCTGCCGGGGCAGTTTCCGCTATTAGTTGGCTATTATCATCGCGAACTGAAAAATCTCATTCTGGTTTCTGCGGGTCTGAATGCGACGTTAAATACCGGCGAACACCAGGTGc                                                           >  1:246967/1‑251 (MQ=255)                                                                                                                                                                        tgctgcCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGGCGCGTTATTGAAGCAGGTAAACCATTTACTTCGTCAGGCCAATCTGCCGGGGCAGTTTCCGCTATTAGTTGGCTATTATCATCGCGAACTGAAAAATCTCATTCTGGTTTCTGCGGGTCTGAATGCGACGTTAAATACCGGCGAACACCAGGTGCAAATCAGTAATg                                               >  1:76598/1‑251 (MQ=255)                                                                                                                                                                         gctgcCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGGCGCGTTATTGAAGCAGGTAAACCATTTACTTCGTCAGGCCAATCTGCCGGGGCAGTTTCCGCTATTAGTTGGCTATTATCATCGCGAACTGAAAAATCTCATTCTGGTTTCTGCGGGTCTGAATGCGACGTTAAATACCAGCGAACACCAGGTGCAATTCAGTAATgg                                              >  2:143998/1‑251 (MQ=255)                                                                                                                                                                               ttGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGGCGCGTTATTGAAGCAGGTAAACCATTTACTTCGTCAGGCCAATCTGCCGGGGCAGTTTCCGCTATTAGTTGGCTATTATCATCGCGAACTGaaa                                                                                                                        >  1:324284/1‑171 (MQ=255)                                                                                                                                                                                          cgcATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGGCGCGTTATTGAAGCAGGTAAACCATTTACTTCGTCAGGCCAATCTGCCGGGGCAGTTTCCGCTATTAGTTGGCTATTATCATCGCGAACTGAAAAATCTCATTCTGGTTTCTGCGGGTCTGAATGCGACGTTAAATACCGGCGAACACCAGGTGCAAATCAGTAATGGTGTTCCGTTAGGCACtt                             <  1:35303/251‑1 (MQ=255)                                                                                                                                                                                                               aCAGGAACAGCTTGCACACCAAAATTAACGGTTGCCAGAGTTGGGCGCGTTATTGAAGCAGGTAAACCATTTACCTCGTCAGGCCAATCTGCCGGGGCAGTTTCCGCTATTAGTTGGCTATTATCATCGCGAACTGAAAAATCTCATTCTGGTTTCTGCGGGTCTGAATGCGACGTTAAATACCGGCGAACACCAGGTGCAAATCAGTAATGGTGTTCCGTTAGGCACTTTAGGTAACGCTTATTTGAAt         <  1:24242/250‑1 (MQ=255)                                                                                                                                                                                                                     aCAGCTTGCAAACCAAAATTAAAGGTTGCCAGAGTTGGGCGCGTTAGTGAAGCAGGTAAACCATTTACTTCGTCAGGCCAATCTGCCGGGGCAGTTTCCGCTATTAGTTGGCTATTATCATCGCGAACTGAAAAATCTCATTCTGGTTTCTGCGGGTCTGAATGCGACGTTAAATACCGGCGAACACCAGGTGCAAATCAGTAATGGTGTTCCGTTAGGCACTTTAGGTAACGCTTATTTGAATCAATTGa  <  2:9780/251‑1 (MQ=255)                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                        GAACTACAACCGCCGGTTCAGCAGGTGATTTCCCATTGCCGGGTTAATTATCGTCAATTGGTTGCCGCGGACAAACCCGGCCTGGTGCTTGATATTGCCGCACTTTCGGAAAACGATCTGGCATTTTATTGCCTTGATGTCACCCGAGCTGGACATAATGGCGTACTTGCTGCCTTGTTATTACGCGCATTGTTTAACGGATTATTACAGGAACAGCTTGCACACCAAAATCAACGGTTGCCAGAGTTGGGCGCGTTATTGAAGCAGGTAAACCATTTACTTCGTCAGGCCAATCTGCCGGGGCAGTTTCCGCTATTAGTTGGCTATTATCATCGCGAACTGAAAAATCTCATTCTGGTTTCTGCGGGTCTGAATGCGACGTTAAATACCGGCGAACACCAGGTGCAAATCAGTAATGGTGTTCCGTTAGGCACTTTAGGTAACGCTTATTTGAATCAATTGA  >  NC_000913/1290716‑1291178

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑