Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,022,686	T→C	L24P (CTA→CCA)	fliQ →	flagellar biosynthesis protein FliQ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,022,686	0	T	C	100.0%	78.1 / NA	23	L24P (CTA→CCA)	fliQ	flagellar biosynthesis protein FliQ
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (15/8);  total (15/8)

GATGGCTGGCAATTGCTGGTCGGTTCGCTGGCGCAGAGCTTTTACAGCTAGAGAGGCAAAATGACACCTGAATCGGTCATGATGATGGGGACTGAAGCGATGAAAGTCGCGCT‑GGCACTGGCTGCCCCGCTATTGTTGGTAGCGTTGGTCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCCGGACCGTGG  >  NC_000913/2022556‑2022819                                                                                                                                    |                                                                                                                                      gATGGCTGGCAATTGCTGGTCGGTTCGCTGGCGCAGAGCTTTTACAGCTAGAGAGGCAAAATGACACCTGAATCGGTCATGATGATGGGGACTGAAGCGATGAAAGTCGCGCT‑GGCACTGGCTGCCCCGCCATTGTTGGt                                                                                                                              >  1:461377/1‑140 (MQ=255)   tggctggcAATTGCTGGTCGGTTCGCTGGCGCAGAGCTTTTACAGCTAGAGAGGCAAAATGACACCTGAATCGGTCATGATGATGGGGACTGAAGCGATGAAAGTCGCGCT‑GGCGCTCGCTGCCACGCCATTGTTGGTAg                                                                                                                            >  1:265948/1‑140 (MQ=255)   tggctggcAATTGCTGGTCGGTTCGCTGGCGCAGAGCTTTTACAGCTAGAGAGGCAAAATGACACCTGAATCGGTCATGATGATGGGGACTGAAGCGATGAAAGTCGCGCT‑GGCACTGGCTGCCCCGCCATTGTTGGTAg                                                                                                                            >  1:615702/1‑140 (MQ=255)      ctggcAATTGCTGGTCGGTTCGCTGGCGCAGAGCTTTTACAGCTAGAGAGGCAAAATGACACCTGAATCGGTCATGATGATGGGGACTGAAGCGATGAAAGTCGCGCT‑GGCACTGGCTGCCCCGCCATTGTTGGTAGCGt                                                                                                                         >  2:490620/1‑140 (MQ=255)             ttGCTGGTCGGTTCGCTGGCGCAGAGCTTTTACAGCTAGAGAGGCAAAATGACACCTGAATCGGTCATGATGATGGGGACTGAAGCGATGAAAGTCGCGCT‑GGCACTGGCTGCCCCGCCATTGTTGGTAGCGTTGGTCAc                                                                                                                  <  1:9473/140‑1 (MQ=255)                    tgggTTGGCGGGCGCAGCGCTTCTACAGCAAGAGAAGCAGAAGGACCCCTGAACGGGTCATGATGAGGGGGCCTGAAGCGAGGAAGGCCGCGCT‑GGCACTGGCCGCCCCGCCATTGTTGGTAGCGTTGGTCACGGGCCtt                                                                                                           <  2:306337/138‑1 (MQ=255)                    tCGGTTCGCTGGCGCAGAGCTTTTACAGCTAGAGAGGCAAAATGACCCCTGAATCGGTCATGATGATGGGGACTGAAGCGATGAAAGCCGCGCT‑GGCACTGGCTGCCCCGCCATTGTTGGTAGCGTTGGTCACGGGCCtt                                                                                                           <  2:529285/140‑1 (MQ=255)                         tCGCGGGCGAAGAGCTTTTACAGCTAGAGAGGAAAAATGACACCTGAATCGGTCATGATGATGGGGACTGAAGCGATGAAAGTCGCGCT‑GGCACTGGCTGCCCCGCCATTGTTGGTAGCGTTGGTCACGGGCCTTatcat                                                                                                      <  1:655042/140‑1 (MQ=255)                          cGCTGGCGCAGAGCTTTTACAGCTAGAGAGGCAAAATGACACCTGAATCGGTCATGATGATGGGGACTGAAGCGATGAAAGTCGCGCT‑GGCACTGGCTGCCCCGCCATTGTTGGTAGCGTTGGTCACGGGCCTTatcatc                                                                                                     >  1:123627/1‑140 (MQ=255)                                               gCTAGAGAGGCAAAATGACACCTGAATCGGTCATGATGATGGGGACTGAAGCGATGAAAGTCGCGCT‑GGCACTGGCTGCCCCGCCATTGTTGGTAGCGTTGGTCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACg                                                                                >  1:142152/1‑140 (MQ=255)                                                    agagGCAAAATGACACCTGAATCGGTCATGATGATGGGGACTGAAGCGATGAAAGTCGCGCT‑GGCACTGGCTGCCCCGCCATTGTTGGTAGCGTTGGTCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGAt                                                                           >  1:336617/1‑140 (MQ=255)                                                        gCAAAATGACACCTGAATCGGTCATGATGATGGGGACTGAAGCGATGAAAGTCGCGCT‑GGCACTGGCTGCCCCGCCATTGTTTGTAGCGTTGGTCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAAc                                                                       >  2:402975/1‑140 (MQ=255)                                                          aaaaTGACACCTGAATCGGTCATGATGATGGGGACTGAAGCGATGAAAGTCGCGCT‑GGCACTGGCTGCCCCGCCATTGTTGGTAGCGTTGGTCACGGGCCTTCTCATCGGGATTTTGAAGGCCGCCACGCAGATTAACGa                                                                     >  1:232091/1‑140 (MQ=255)                                                               acccccggAATCGGTCTGGATGGAGGGGACTGAAGCGAGGAAAAGCG‑GCTGGGCCCGGGGTCGCCCGCCATTGTTGGTAGCGTTGGGCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGa                                                                <  2:461377/133‑1 (MQ=255)                                                                   ccTGAATCGGTCATGATGATGGGGACTGAAGCGATGAAAGTCGCGCT‑GGCACTGGCTGCCCCGCCATTGTTGGTAGCGTTGGTCACGGGCCTTATCATCAGTTTTTTGCATGCCGCCACGCAGAGTAACGAAATGACGCt                                                            >  1:304262/1‑140 (MQ=255)                                                                                      tgGGGACTGAAGCGATGAAAGTCGCGCT‑GGCACTGGCTGCCCCGCCATTGTTGGTAGCGTTGGTCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAatc                                         >  1:31593/1‑140 (MQ=255)                                                                                          gACTGAAGCGATGAAGGTCGCGCT‑GCCACTGGCTGCCCCGCCATTGTTGGTAGCGTTGGTCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCg                                     <  1:302713/140‑1 (MQ=255)                                                                                                    atgagggTCGGGCG‑GGCACTGGCTGCCCCGCCATTGTTGGTAGCGTTGGTCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTAt                           <  2:142152/134‑1 (MQ=255)                                                                                                    aTGAAAGTCGCGCT‑GGCACTGGCTGCCCCGCCATTGTTGGTAGCGTTGGTCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACACTGTCGTTTATTGCGAAAATCATCGCCGTATTTAt                           >  2:310226/1‑140 (MQ=255)                                                                                                       aaaGTCGCGCT‑GGCACTGGCTGCCCAGCCCTTGTTGGCAGCGTTGGTCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGc                        <  1:184852/140‑1 (MQ=255)                                                                                                              cgcT‑GGCACTGGCTGCCCCGCCATTGTTGGTAGCGTTGGTCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCattatt                 >  2:482969/1‑140 (MQ=255)                                                                                                                        tGGCTCCCCCGCCATTGTTGGTAGCGTTGGTCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTTTTTATCGCCATTATTATTGCCGGa        <  2:615702/140‑1 (MQ=255)                                                                                                                         ggCTGCCCCGCCATTGTTGGTAGCGTTGGTCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGACGTTTTTATCGCCTTTATTATTGCCGGAc       >  1:245128/1‑140 (MQ=255)                                                                                                                             gCCCCGCCATTGTTGGTAGCGTTGGTCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCCGGACCGTg   <  1:490620/140‑1 (MQ=255)                                                                                                                              ccccGCCATTGTTGGTAGCGTTGGTCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCCGGACCGTgg  >  2:8562/1‑140 (MQ=255)                                                                                                                                    |                                                                                                                                      GATGGCTGGCAATTGCTGGTCGGTTCGCTGGCGCAGAGCTTTTACAGCTAGAGAGGCAAAATGACACCTGAATCGGTCATGATGATGGGGACTGAAGCGATGAAAGTCGCGCT‑GGCACTGGCTGCCCCGCTATTGTTGGTAGCGTTGGTCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCCGGACCGTGG  >  NC_000913/2022556‑2022819

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: ‑