Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,014,277	A→G	E237G (GAA→GGA)	fliM →	flagellar motor switch protein FliM

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,014,277	0	A	G	100.0%	145.4 / NA	40	E237G (GAA→GGA)	fliM	flagellar motor switch protein FliM
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (24/16);  total (24/16)

CCTCGCCGAACGACATTGTGGTTAACACGCCGTTCCATGTGGAGATTGGCAA‑CCTGACCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGAAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGCCAGGTGCAGCATTCACAGCTGGAGCTGGTCGCCAACTTTGCCGATATCTCGCTACGCCTGTCGCAGATTTTAAAACTGAA  >  NZ_CP009273/2014145‑2014403                                                                                                                                      |                                                                                                                               ccTCGCCGAACGACATTGTGGTTAACACGCCGTTCCATGTGGAGATTGGCAA‑CCTGACCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTc                                                                                                                          >  1:146638/1‑139 (MQ=255)    cGCCGAACGACATTGTGGTTAACACGCCGTTCCATGTGGAGATTGGCAA‑CCTGACCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTcgcg                                                                                                                       >  2:216742/1‑139 (MQ=255)       cGAACGACATTGTGGTTAACACGCCGTTCCATGTGGAGATTGGCAA‑CCTGACCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTaa                                                                                                                    >  2:22722/1‑139 (MQ=255)         aaggaaaTTGGGGTAAACACGCCGTTCCATGGGGAGATGGGCAA‑CCTGACCGGCGAATTTAATATCGGCCTGCAATTAAGAATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATg                                                                                                                  <  1:190489/133‑1 (MQ=255)         aaCGACTTGGTGTTTAACCCGCCGTCCCATGTGGAGTTTGCCAC‑CCGGCCCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGGGCCGCTACGGGAATTGTTGTTTACCCCGCCGCTGGGAAACTCGCGTAATg                                                                                                                  <  2:789217/139‑1 (MQ=255)         aaCGACATTGTGTTTAACACGCCGTTCCATGTGGAGATTGGCAA‑CCTGACCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATg                                                                                                                  <  1:216742/139‑1 (MQ=255)         aaCGACATGGGGGTAACCACGCCGTCCCAGGGGGAGA‑TGGCAACCCTGACCGGCGAATTAAATATCGCCCTCCCTTCCAGCATGATCGGGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATg                                                                                                                  <  2:500938/139‑1 (MQ=255)                 tgtgGTTAACACGCCGTTCCATGTGGAGATTGGCAA‑CCTGACCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGAt                                                                                                             >  2:94726/1‑136 (MQ=255)                 tgtgGTTAACACGCCGTTCCATGTGGAGATTGGCAA‑CCTGACCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGAt                                                                                                             >  1:522114/1‑136 (MQ=255)                 tgtgGTTAACACGCCGTTCCATGTGGAGATTGGCAA‑CCTGACCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGAt                                                                                                             >  1:789217/1‑136 (MQ=255)                        aaCACGCCGTTCCATGTGGAGATTGGCAA‑CCTGACCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGgc                                                                                                   >  2:282253/1‑139 (MQ=255)                        aaCACGCCGTGCCATGGGGAGATTGACAC‑CCTGCCCGGCGATTTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGTTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTgg                                                                                                    <  2:89425/138‑1 (MQ=255)                             gCCGTTCCATGTGGAGATTGGCAA‑CCTGACCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGa                                                                                               >  1:794314/1‑138 (MQ=255)                             gCCGTTCCATGTGGAGATTGGCAA‑CCTGACCGACGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGa                                                                                               >  1:744001/1‑138 (MQ=255)                                  tCCATGTGGAGATTGGCAA‑CCTGACCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCt                                                                                         >  2:739322/1‑139 (MQ=255)                                    cATGTGGAGATTGGCAA‑CCTGACCGGCGATTTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTg                                                                                        <  1:75584/138‑1 (MQ=255)                                      tgtgGAGATTGGCAA‑CCTGACCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATg                                                                                                                  >  1:242907/1‑110 (MQ=255)                                      tgtgGAGATTGGCAA‑CCTGACCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTg                                                                                     >  2:706080/1‑139 (MQ=255)                                      tgtgGAGATTGGCAA‑CCTGACCGGCGAATTTAATATCTGCCTCCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATg                                                                                                                  <  2:242907/110‑1 (MQ=255)                                         ggAGATTGGCAA‑CCTGACCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTgcgc                                                                                  >  2:464585/1‑139 (MQ=255)                                          gagaTTGGCAA‑CCTGACCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGcc                                                                                 <  1:22722/139‑1 (MQ=255)                                                 gCAA‑CCTGACCGGCAAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGCCAGGTgc                                                                           <  1:464585/138‑1 (MQ=255)                                                    a‑CCTGACCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGCCAGGTgcagca                                                                       >  2:594036/1‑139 (MQ=255)                                                       cTGACCGGCAAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTACCCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGCCAGGTGCAGCAtt                                                                     <  1:800219/139‑1 (MQ=255)                                                          aCCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGCCAGGTGCAGCATTca                                                                   >  2:94735/1‑138 (MQ=255)                                                                             gcctgccATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGCCAGGTGCAGCATTCACAGCTGGAGCTGGTCGCCaa                                               >  2:127232/1‑139 (MQ=255)                                                                              cctgccATTCAGCTTGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGcc                                                                                 <  1:469001/104‑1 (MQ=255)                                                                              cctgccATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGcc                                                                                 >  2:469001/1‑104 (MQ=255)                                                                                   cATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGCCAGGTGCAGCATTCACAGCTGGAGCTGGTCGCCAACTTTGc                                         >  2:814500/1‑139 (MQ=255)                                                                                         gCATGATGGCGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGCCAGGTGCAGCATTCACAGCTGGAGCTGGTCGCCAACTTTGCCGatat                                   <  2:74328/139‑1 (MQ=255)                                                                                               tCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGCCAGGTGCAGCATTCACAGCTGGAGCTGGTCGCCAACTTTGCCGATATCTCGc                              >  2:188450/1‑138 (MQ=255)                                                                                                         aCGGGAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGCCAGGTGCAGCATTCACAGCTGGAGCTGGTCGCCAACTTTGCCGATATCTCGCTACGCCTGTCg                   >  1:87223/1‑139 (MQ=255)                                                                                                           gggAATTGTTGGTTACCCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGCCAGGTGCAGCATTCACAGCTGGAGCTGGTCGCCAACTTTGCCGATATCTCGCTACGCCTGTCGCa                 <  1:837521/139‑1 (MQ=255)                                                                                                           gggAATTGTTGGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGCCAGGTGCAGCATTCACAGCTGGAGCTGGTCGCCAACTTTGCCGATATCTCGCTACGCCTGTCGCa                 <  2:794314/139‑1 (MQ=255)                                                                                                                  gttgGTTAACCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGCCAGGTGCAGCATTCACAGCTGGAGCTGGTCGCCAACTTTGCCGATATCTCGCTACGCCTGTCGCAGAtttt           >  2:57858/1‑138 (MQ=255)                                                                                                                          ccccGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGCCAGGTGCAGCATTc                                                                    <  2:669055/72‑1 (MQ=255)                                                                                                                          aCCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGCCAGGTGCAGCATTc                                                                    >  1:669055/1‑73 (MQ=255)                                                                                                                          aCCCGCCGCTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGCCAGGTGCAGCATTCACAGCTGGAGCTGGTCGCCAACTTTGCCGATATCTCGCTACGCCTGTCGCAGATTTTAAAACTGaa  >  1:486075/1‑139 (MQ=255)                                                                                                                                cgcTGGGAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGCCAGGTGCAGCATTc                                                                    >  2:160805/1‑67 (MQ=255)                                                                                                                                cgcTGGGAAACTCGCGTAATGAAGAACAGAACTGGCGCGATAACCTGGTGCGCCAGGTGCAGCATTc                                                                    <  1:160805/67‑1 (MQ=255)                                                                                                                                      |                                                                                                                               CCTCGCCGAACGACATTGTGGTTAACACGCCGTTCCATGTGGAGATTGGCAA‑CCTGACCGGCGAATTTAATATCTGCCTGCCATTCAGCATGATCGAGCCGCTACGGGAATTGTTGGTTAACCCGCCGCTGGAAAACTCGCGTAATGAAGATCAGAACTGGCGCGATAACCTGGTGCGCCAGGTGCAGCATTCACAGCTGGAGCTGGTCGCCAACTTTGCCGATATCTCGCTACGCCTGTCGCAGATTTTAAAACTGAA  >  NZ_CP009273/2014145‑2014403

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑