Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,977,418	T→C	N143D (AAT→GAT)	flhC ←	flagellar class II regulon transcriptional activator, with FlhD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,977,418	0	T	C	100.0%	142.2 / NA	38	N143D (AAT→GAT)	flhC	flagellar class II regulon transcriptional activator, with FlhD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (22/16);  total (22/16)

CATCCAGCAGTTGTGGGATAATATCGGCAGGATTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTTGTGGGCACTGTTCAAGGTATAAAC  >  NC_000913/1977289‑1977546                                                                                                                                  |                                                                                                                                 cATCCAGCAGTTGTGGGATAATATCGGCAGGATTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCgca                                                                                                                         >  1:498071/1‑139 (MQ=255)   tCCAGCAGTTGTGGGATAATATCGGCAGGATTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCgcagc                                                                                                                       >  1:1241297/1‑139 (MQ=255)     cagcagTTGTGGGATAATATCGGCAGGATTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGcagcag                                                                                                                     >  1:587310/1‑139 (MQ=255)                     atatCGGCAGGATTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGtt                                                                                                     >  2:760329/1‑139 (MQ=255)                      tatCGGCAGGATTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTg                                                                                                    >  2:1063866/1‑139 (MQ=255)                            cAGGATTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTaa                                                                                              >  1:336392/1‑139 (MQ=255)                                aTTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCa                                                                                          >  1:455797/1‑139 (MQ=255)                                           gTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACaaa                                                                               <  2:1080795/139‑1 (MQ=255)                                            tttACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAAc                                                                              <  1:885817/139‑1 (MQ=255)                                              tACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCg                                                                            >  1:406661/1‑139 (MQ=255)                                              tACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCg                                                                            <  2:1241297/139‑1 (MQ=255)                                                cGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCa                                                                          >  2:337820/1‑139 (MQ=255)                                                   cTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCa                                                                       <  2:336392/139‑1 (MQ=255)                                                   cTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCa                                                                       <  2:498071/139‑1 (MQ=255)                                                            gCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAgg                                                              >  2:516493/1‑139 (MQ=255)                                                             cccGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACGGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGc                                                             <  1:952419/139‑1 (MQ=255)                                                             cccGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACGGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGc                                                             >  2:952419/1‑139 (MQ=255)                                                             cccGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCa                                                                       <  1:745466/129‑1 (MQ=255)                                                             cccGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCa                                                                       >  2:745466/1‑129 (MQ=255)                                                             cccGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGc                                                             >  1:1125031/1‑139 (MQ=255)                                                             cccGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGc                                                             >  2:919548/1‑139 (MQ=255)                                                             cccGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGc                                                             >  2:398631/1‑139 (MQ=255)                                                               cGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGTAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCAc                                                           >  2:1152795/1‑139 (MQ=255)                                                                       cGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTcaa                                                                                   >  1:1149580/1‑107 (MQ=255)                                                                       cGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTcaa                                                                                   <  2:1149580/107‑1 (MQ=255)                                                                       cGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAAt                                                   >  1:450347/1‑139 (MQ=255)                                                                             aCATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCcagc                                             <  1:919548/139‑1 (MQ=255)                                                                              cATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCcagca                                            <  1:805933/139‑1 (MQ=255)                                                                                      gCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCct                                    <  2:1125031/139‑1 (MQ=255)                                                                                        aGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCcttc                                  >  1:135654/1‑139 (MQ=255)                                                                                           cAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCttcttc                               <  2:406661/139‑1 (MQ=255)                                                                                             aaGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTg                             <  1:398631/139‑1 (MQ=255)                                                                                                  gCCAACAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTtgt                        <  1:337820/139‑1 (MQ=255)                                                                                                       cAGGCTGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTTGTGGGCa                   <  1:1063866/139‑1 (MQ=255)                                                                                                            tGGTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTTGTGGGCACTGtt              <  1:760329/139‑1 (MQ=255)                                                                                                             ggTGAGCGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTTGTGGGCACTGTTc             >  2:489287/1‑139 (MQ=255)                                                                                                                   cGTGGGTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTTGTGGGCACTGTTCAAGGta       >  1:52872/1‑139 (MQ=255)                                                                                                                        gTAATAAAATCGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTTGTGGGCACTGTTCAAGGTATAAAc  >  2:716395/1‑139 (MQ=255)                                                                                                                                  |                                                                                                                                 CATCCAGCAGTTGTGGGATAATATCGGCAGGATTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTTGTGGGCACTGTTCAAGGTATAAAC  >  NC_000913/1977289‑1977546

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑