Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,022,885	G→A	*90* (TAG→TAA)	fliQ →	flagellar biosynthesis protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,022,885	0	G	A	100.0%	192.2 / NA	59	*90* (TAG→TAA)	fliQ	flagellar biosynthesis protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (30/29);  total (30/29)

CGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCCGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAGCCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGCCGTTACTGCGCGTGCTGGCGCTGATCTCCACCGCGCCGATTCTGAGCGAACGCAG  >  NC_000913/2022750‑2023002                                                                                                                                        |                                                                                                                      cGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCCGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCg                                                                                                                    <  1:1628258/139‑1 (MQ=255)                                          ttATCGCCATTATTATTGCCGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGt                                                                           <  2:1356767/139‑1 (MQ=255)                                                 cATTATTATTGCCGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAAc                                                                                          >  1:1026063/1‑117 (MQ=255)                                                 cATTATTATTGCCGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAAc                                                                                          <  2:1026063/117‑1 (MQ=255)                                                           gCCGGACCGTGGATGCTCAATCTGTTGTTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAATCTGTACTTCTgg                                                          >  2:1009582/1‑139 (MQ=255)                                                           gCCGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACt                                                                                                                >  2:1424096/1‑85 (MQ=255)                                                           gCCGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACt                                                                                                                <  1:1424096/85‑1 (MQ=255)                                                           gCCGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGc                                                                                              >  1:1055014/1‑103 (MQ=255)                                                           gCCGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGc                                                                                              <  2:1055014/103‑1 (MQ=255)                                                                aCCGTGGATGCTCAATCTGTTGCTGGATTACGTCCTCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCGATCCTGGTTAAACCTGTACTTCTGGCCGtt                                                     >  2:337420/1‑139 (MQ=255)                                                                aCCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGCCGtt                                                     >  2:643408/1‑139 (MQ=255)                                                                 ccGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGt                                                                  >  2:189828/1‑125 (MQ=255)                                                                 ccGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGt                                                                  <  1:189828/125‑1 (MQ=255)                                                                    tGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTg                                                                   >  1:1645567/1‑121 (MQ=255)                                                                    tGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTg                                                                   <  2:1645567/121‑1 (MQ=255)                                                                         gCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGt                                                                                                     <  2:756208/82‑1 (MQ=255)                                                                         gCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGt                                                                                                     >  1:756208/1‑82 (MQ=255)                                                                          cTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACt                                                                                                                >  1:479042/1‑70 (MQ=255)                                                                          cTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACt                                                                                                                <  2:479042/70‑1 (MQ=255)                                                                              aTCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAAc                                                                                          >  2:1183540/1‑88 (MQ=255)                                                                              aTCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAAc                                                                                          <  1:1183540/88‑1 (MQ=255)                                                                              aTCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGCCGTTACTGCGCGTg                                           >  1:1318738/1‑135 (MQ=255)                                                                              aTCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGCCGTTACTGCGCGTg                                           <  2:1318738/135‑1 (MQ=255)                                                                               tCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAg                                                                                               >  2:420630/1‑82 (MQ=255)                                                                               tCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAg                                                                                               <  1:420630/82‑1 (MQ=255)                                                                                    tGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATcc                                                                               >  1:970816/1‑93 (MQ=255)                                                                                    tGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGCCGTTACTGCGCGTGCTGgcg                                     <  1:721650/135‑1 (MQ=255)                                                                                    tGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGCCGTTACTGCGCGTGCTGgcg                                     >  2:721650/1‑135 (MQ=255)                                                                                    tGCTGGATTACGTCCGCACCTCGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATcc                                                                               <  2:970816/93‑1 (MQ=255)                                                                                         gATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAg                                                                                                       <  1:1643702/64‑1 (MQ=255)                                                                                         gATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAg                                                                                                       >  2:1643702/1‑64 (MQ=255)                                                                                                    cACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATgg                                                                                     >  2:540039/1‑71 (MQ=255)                                                                                                    cACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATgg                                                                                     <  1:540039/71‑1 (MQ=255)                                                                                                    cACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGCCGTTACTGCGCGTGCTGGCGCTGATCTCCACCGCGCCGAt                 <  1:643408/139‑1 (MQ=255)                                                                                                      ccTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTCCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGCCGTTACTGCGCGTGCTGGCGCTGATCTCCACCGCGCCGATTc               <  1:1009582/139‑1 (MQ=255)                                                                                                          gTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGt                                                                           >  2:1385289/1‑75 (MQ=255)                                                                                                          gTTCACGAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGt                                                                           <  1:1385289/75‑1 (MQ=255)                                                                                                           ttCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAAc                                                                                          <  1:233862/59‑1 (MQ=255)                                                                                                           ttCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAAc                                                                                          >  2:233862/1‑59 (MQ=255)                                                                                                           ttCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACtt                                                              <  1:686873/87‑1 (MQ=255)                                                                                                           ttCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACtt                                                              >  2:686873/1‑87 (MQ=255)                                                                                                                tAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAAc                                                                                          <  1:1547039/54‑1 (MQ=255)                                                                                                                tAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAAc                                                                                          >  2:1547039/1‑54 (MQ=255)                                                                                                                 aaCCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGCCGTTACTGCGCGTGCTGGCGCTGATCTCCACCGCGCCGATTCTGAGCGAACg     >  2:1466189/1‑138 (MQ=255)                                                                                                                 aaCCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGCCGTTACTGCGCGTGCTGGCGCTGATCTCCACCGCGCCGATTCTGAGCGAACg     <  1:1466189/138‑1 (MQ=255)                                                                                                                 aaCCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGCCGTTACTGCGCGTGCTGGCGCTGATCTCCACCGCGCCGATTCTGAGCGAACGc    >  1:1010178/1‑139 (MQ=255)                                                                                                                   ccTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATgg                                                                                     <  2:1498371/56‑1 (MQ=255)                                                                                                                   ccTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATgg                                                                                     >  1:1498371/1‑56 (MQ=255)                                                                                                                   ccTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGCCGTTACTGCGCGTGCTGGCGCTGATCTCCACCGCGCCGATTCTGAGCGAACGCAg  >  1:986908/1‑139 (MQ=255)                                                                                                                       ccGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATgg                                                                                     >  2:4815/1‑52 (MQ=255)                                                                                                                       ccGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATgg                                                                                     <  1:4815/52‑1 (MQ=255)                                                                                                                              tcatcGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATgg                                                                                     >  2:1186759/1‑45 (MQ=255)                                                                                                                              tcatcGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATgg                                                                                     <  1:1186759/45‑1 (MQ=255)                                                                                                                              tcatcGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGCCGTTACTGCGCGTGCTGGCGCTGATCTCCACCGCGCCGATTCTGAGCGAACGCa   <  1:709832/127‑1 (MQ=255)                                                                                                                              tcatcGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGCCGTTACTGCGCGTGCTGGCGCTGATCTCCACCGCGCCGATTCTGAGCGAACGCa   >  2:709832/1‑127 (MQ=255)                                                                                                                                 tcGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGCCGTTACTGCGCGTGCTGgcg                                     >  2:602412/1‑90 (MQ=255)                                                                                                                                 tcGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGCCGTTACTGCGCGTGCTGgcg                                     <  1:602412/90‑1 (MQ=255)                                                                                                                                  cGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGcc                                                        >  2:501527/1‑70 (MQ=255)                                                                                                                                  cGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGcc                                                        <  1:501527/70‑1 (MQ=255)                                                                                                                                        |                                                                                                                      CGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCCGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAGCCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCTGGCCGTTACTGCGCGTGCTGGCGCTGATCTCCACCGCGCCGATTCTGAGCGAACGCAG  >  NC_000913/2022750‑2023002

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: ‑