Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,978,083	+A	coding (115/351 nt)	flhD ←	DNA‑binding transcriptional dual regulator FlhD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,978,083	1	.	A	100.0%	69.8 / NA	21	N39Y (AAT→TAT)	flhD	DNA‑binding transcriptional dual regulator FlhD
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base A (8/13);  total (8/13)

TCTTGCGCAGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGTAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATT‑TATGCCGAGACGAAACATAGCGGACGCTTTGTCCTGAACAATCAAACGCTGTGCAAGTAGTAAATATGACAAGTTGATGTCATAAATGTGTTTCAGCAACTCGGAGGTATGCATTATTCCCACCCAGAATAACCAACTTTATTTTTATGCGGTTTCACCGCACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACC  >  NC_000913/1977858‑1978324                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                  tCTTGCGCAGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGTAATCGTCTGGTGGCTGTCAAAACGGAGGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTATATGCCGAGACGAAACATAGCgg                                                                                                                                                                                                                            >  2:47613/1‑250 (MQ=255)    tGCGCAGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGTAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTATATGCCGAGACGAAACATAGCGGAc                                                                                                                                                                                                                          <  1:208836/249‑1 (MQ=255)         aGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGTAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTATATGCCGAGACGAAACATAGCGGACGCTTTGt                                                                                                                                                                                                                   >  2:163654/1‑251 (MQ=255)         aGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGTAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTATATGCCGAGACGAAACATAGCGGACGCTTTGt                                                                                                                                                                                                                   <  2:267091/251‑1 (MQ=255)                                  catTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGAGGGAATCTTGCGTCAACTGAGTAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTATATGCCGAGAAGAAACATAGCGGACGCTTTGTCCTGAACAATCAAACGCTGTGCa                                                                                                                                                                                            >  1:161048/1‑249 (MQ=255)                                                gtTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGTAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTATATGCCGAGACGAAACATAGCGGACGCTTTGTCCTGAACAATCAAACGCTGTGCAAGTAGGAAATATGACa                                                                                                                                                                            <  1:231139/251‑1 (MQ=255)                                                                    aTGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGTAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTATATGCCGAGACGAAACATAGCGGACGCTTTGTCCTGAACAATCAAACGCTGTGCAAGTAGTAAATATGACAAGTTGATGTCATAAAtgtg                                                                                                                                                         <  2:54386/250‑1 (MQ=255)                                                                                                      tGCGTCAACTGAGTAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTATATGCCGAGACGAAACATAGCGGACGCTTTGTCCTGAACAATCAAACGCTGTGCAAGTAGTAAATATGACAAGTTGATGTCATAAATGTGTTTCAGCAACGCGTAGGTATGCATTATTcccacc                                                                                                                       <  2:15172/250‑1 (MQ=255)                                                                                                         gTCAACTGAGTAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTATATGCCGAGACGAAACATAGCGGACGCTTTGTCCTGAACAATCAAACGCTGTGCAAGTAGTAAATATGACAAGTTGATGTCATAAATGTGTTTCAGCAACTCGGAGGTATGCATTATTCCCACCCAGa                                                                                                                   <  2:197586/251‑1 (MQ=255)                                                                                                                                  tGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTATATGCCGAGACGAAACATAGCGGACGCTTTGTCCTGAACAATCAAACGCTGTGCAAGTAGTAAATATGACAAGTTGATGTCATAAATGTGTTTCAGCAACTCGGAGGTATGCATTATTCCCACCCAGAATAACCAACTTTATTTTTATGCGGt                                                                                          >  1:223782/1‑251 (MQ=255)                                                                                                                                                                tGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTATATGCCGAGACGAAACATAGCGGACGCTTTGTCCTGAACAATCAAACGCTGTGCAAGTAGTAAATATGACAAGTTGATGTCATAAATGTGTTTCAGCAACTCGGAGGTATGCATTATTCCCACCCAGAATAACCAACTTTATTTTTATGCGGTTTCACCGCACCCCGTGATGTCGCCGGGaa                                                             <  2:192088/250‑1 (MQ=255)                                                                                                                                                                     tCTGCCAGCTTAACCATTTGCGGTAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTATATGCCGAGACGAAACATAGCGGACGCTTTGTCCTGAACAATCAAACGCTGTGCAAGTAGTAAATATGACAAGTTGATGTCATAAATGTGTTTCAGCAACTCGGAGGTATGCATTATTCCCACCTATAATAACCAACTTTATTTTTATGCGGTTTCACCGCTCCCCGTGATGTCGCCGGGAATcccc                                                        <  2:258758/250‑1 (MQ=255)                                                                                                                                                                     tCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTATATGCCGAGACGAAACATAGCGGACGCTTTGTCCTGAACAATCAAACGCTGTGCAAGTAGTAAATATGACAAGTTGATGTCATAAATGTGTTTCAGCAACTCGGAGGTATGCATTATTCCCACCCAGAATAACCAACTTTATTTTTATGCGGTTTCACCGCACCCCGTGATGTCGCCGGGAAGcccc                                                        <  1:77516/250‑1 (MQ=255)                                                                                                                                                                        gCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTATATGCCGAGACGAAACATAGCGGACGCTTTGTCCTGAACAATCAAACGCTGTGCAAGTAGTAAATATGACAAGTTGATGTCATAAATGTGTTTCAGCAACTCGGAGGTATGCATTATTCCCACCCAGAATAACCAACTTTATTTTTATGCGGTTTCACCGCACCCCGTGATGTCGCCGGGAAGCCCCg                                                       <  1:163654/248‑1 (MQ=255)                                                                                                                                                                         ccAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTATATGCCGAGACGAAACATAGCGGACGCTTTGTCCTGAACAATCAAACGCTGTGCAAGTAGTAAATATGACAAGTTGATGTCATAAATGTGTTTCAGCAACTCGGAGGTATGCATTATTCCCACCCAGAATAACCAACTTTATTTTTATGCGGTTTCACCGCACCCCGTGATGTCGCCGGGAAGCCCCGGTaa                                                   <  1:47613/251‑1 (MQ=255)                                                                                                                                                                               tAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTATATGCCGAGACGAAACATAGCGGACGCTTTGTCCTGAACAATCAAACGCTGTGCAAGTAGTAAATATGACAAGTTGATGTCATAAATGTGTTTCAGCAACTCGGAGGTATGCATTATTCCCACCCAGAATAACCAACTTTATTTTTATGCGGTTTCACCGCACCCCGTGATGTCGCCGGGAAGCCCCGGTaaaaaa                                               <  2:4794/249‑1 (MQ=255)                                                                                                                                                                                                   aGTGCCGCTACCGTTGTCGCCATTTCTTCATTATCTGCCGAGACGAAACATAGCGGACGCTTTGTCCTGAACAATCAAACGCTGTGCAAGTAGTAAATATGACAAGTTGATGTCATAAATGTGTTTCAGCAACTCGGAGGTATGCATTATTCCCACCCAGAATAACCAACTTTATTTTTATGCGGTTTCACCGCACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGc                         >  2:66987/1‑251 (MQ=255)                                                                                                                                                                                                              cGTTGTCGCCATTTCTTCATTATATGCCGAGACGAAACATAGCGGACGCTTTGTCCTGAACAATCAAACGCTGTGCAAGTAGTAAATATGACAAGTTGATGTCATAAATGTGTTTCAGCAACTCGGAGGTATGCATTATTCCCACCCAGAATAACCAACTTTATTTTTATGCGGTTTCACCGCACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGc               >  2:48118/1‑250 (MQ=255)                                                                                                                                                                                                                ttGTCGCCATTTCTTCATTATATGCCGAGACGAAACATAGCGGACGCTTTGTCCTGAACAATCAAACGCTGTGCAAGTAGTAAATATGACAAGTTGATGTCATAAATGTGTTTCAGCAACTCGGAGGTATGCATTATTCCCACCCAGAATAACCAACTTTATTTTTATGCGGTTTCACCGCACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAAt            >  1:181937/1‑251 (MQ=255)                                                                                                                                                                                                                    cGCCATTTCTTCATTATATGCCGAGACGAAACATAGCGGACGCTTTGTCCTGAACAATCAAACGCCGTGCAAGTAGTAAATATGACAAGTTGATGTCATAAATGTGTTTCAGCAACTCGGAGGTATGCATTATTCCCACCCAGAATAACCAACTTTATTTTTATGCGGTTTCACCGCACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAg         <  2:83037/250‑1 (MQ=255)                                                                                                                                                                                                                          ttcttcATTATATGCCGAGACGAAACATAGCGGACGCTTTTTCCTGAACAATCAAACGCTGTGCAAGTAGTAAATATGACACGTTGATGTCATAAATGTGTTTCAGCAACTCGGAGGTATGCATTATTCCCACCCAGAATAACCAACTTTATTTTTATGCGGTTTCACCGCACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCCTTAGAATAGTTGCGATAAGCTGCAATAAGCAGAacc  >  2:74052/1‑251 (MQ=255)                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                  TCTTGCGCAGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGTAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATT‑TATGCCGAGACGAAACATAGCGGACGCTTTGTCCTGAACAATCAAACGCTGTGCAAGTAGTAAATATGACAAGTTGATGTCATAAATGTGTTTCAGCAACTCGGAGGTATGCATTATTCCCACCCAGAATAACCAACTTTATTTTTATGCGGTTTCACCGCACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACC  >  NC_000913/1977858‑1978324

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑