Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,014,272	T→C	R348R (CGT→CGC)	fliF →	flagellar basal‑body MS‑ring and collar protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,014,272	0	T	C	100.0%	154.2 / NA	43	R348R (CGT→CGC)	fliF	flagellar basal‑body MS‑ring and collar protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (16/27);  total (16/27)

CGGTTATCCGGGCGGCGTACCGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACAAAACCTTGCCAGATGGCAAACCG  >  NC_000913/2014137‑2014407                                                                                                                                        |                                                                                                                                        cGGTTATCGGGGGGGCGTACGGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGAAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCCGCAATAGTGGGCCGCgcagca                                                                                                                                     <  2:769355/140‑1 (MQ=255)          ggggggCGTACGGGGGGCGTTGTCGAATCACCCGGCACCGGCAAAAAACGCGCCAATCAGCCCCCCCCGGGAAAATCAAAAAAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGa                                                                                                                            <  2:526693/140‑1 (MQ=255)              ggcgTACCGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGa                                                                                                                        <  2:107215/140‑1 (MQ=255)               gcgTACCGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGaa                                                                                                                       <  2:195278/140‑1 (MQ=255)               gcgTACCGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGaa                                                                                                                       <  1:999286/140‑1 (MQ=255)                 gtccggggggCGTTGTCGAATCAACCGGCACCTGCAAATAACGCGCAAATCAGCACGCCCCCGGAAAATAAAAAAAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAAc                                                                                                                     <  2:766445/135‑1 (MQ=255)                 gTACCGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAAc                                                                                                                     <  2:282687/140‑1 (MQ=255)                  tcccGGGGGCGTTGTCAAACCAACCGGCCCCTGCAAATAACGCGCAAACCAGCCCGCCCCCGGAAAATCAAAAAAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAAcc                                                                                                                    <  2:855329/138‑1 (MQ=255)                     cGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCTCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGt                                                                                                                 <  1:471710/140‑1 (MQ=255)                          gCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTa                                                                                                            >  2:4180/1‑140 (MQ=255)                          gCGATGCCGAATCAACCGGCACCTGCGAATAACCCGCCACTCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTa                                                                                                            >  2:435947/1‑140 (MQ=255)                                        aCCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCa                                                                                              >  1:981330/1‑140 (MQ=255)                                         ccGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCAc                                                                                             >  2:14840/1‑140 (MQ=255)                                          cGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCAcc                                                                                            >  1:266781/1‑140 (MQ=255)                                           ggCACCTGCGAATAACGCGCCAATCAGCCCGCCCCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCa                                                                                           <  2:290652/140‑1 (MQ=255)                                           ggCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCa                                                                                           <  1:903393/140‑1 (MQ=255)                                              aCCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTc                                                                                        <  1:4180/140‑1 (MQ=255)                                               ccTGCGAATAACGCGCAAATCAGCACGCCTCCGGCAAAAAAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCg                                                                                       <  1:1065628/140‑1 (MQ=255)                                                  gCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCa                                                                                    >  2:1071295/1‑140 (MQ=255)                                                    gAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATa                                                                                  <  1:29958/140‑1 (MQ=255)                                                          cgcgCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCaaaa                                                                            >  1:524957/1‑140 (MQ=255)                                                          cgcgCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCaaaa                                                                            >  1:276296/1‑140 (MQ=255)                                                            cgcCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATg                                                                          >  1:96588/1‑140 (MQ=255)                                                                 aTCAGCCCGCCCCCGACAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGt                                                                     <  1:810769/140‑1 (MQ=255)                                                                           cTCGGGAAAATAAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGAtgtg                                                           <  1:435947/140‑1 (MQ=255)                                                                           cTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGAtgtg                                                           >  2:407935/1‑140 (MQ=255)                                                                             ccGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCa                                                         >  1:263862/1‑140 (MQ=255)                                                                              cGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCaa                                                        <  1:830306/140‑1 (MQ=255)                                                                                     tCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGt                                                 <  2:524957/140‑1 (MQ=255)                                                                                     tCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGt                                                 <  2:981330/140‑1 (MQ=255)                                                                                     tCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGt                                                 >  1:961752/1‑140 (MQ=255)                                                                                     aaaaaaaaACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGt                                                 <  2:276296/138‑1 (MQ=255)                                                                                      aaaaaTAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTc                                                <  1:1071295/139‑1 (MQ=255)                                                                                              ccGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCgg                                        <  1:531108/140‑1 (MQ=255)                                                                                              ccGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCgg                                        <  1:14840/140‑1 (MQ=255)                                                                                                 ccAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCg                                     >  1:551174/1‑140 (MQ=255)                                                                                                    gctgcagGCGAGCACCACCAGCAATAGTGGTCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCgtgg                                  <  2:666360/137‑1 (MQ=255)                                                                                                      agcagGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCgtggtg                                <  2:266781/140‑1 (MQ=255)                                                                                                      agcagGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCgtggtg                                <  2:15274/140‑1 (MQ=255)                                                                                                      agcagGCGAGCACCACCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCgtggtg                                <  2:96588/140‑1 (MQ=255)                                                                                                                caccacCAGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACaaaa                      >  1:230699/1‑140 (MQ=255)                                                                                                                     ccaGCAATAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACAAAACCTTg                 >  2:666196/1‑140 (MQ=255)                                                                                                                            tAGTGGGCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACAAAACCTTGCCAGATg          >  1:469774/1‑140 (MQ=255)                                                                                                                                gggCCGCGCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACAAAACCTTGCCAGATGGCaa      <  2:263862/140‑1 (MQ=255)                                                                                                                                    cgcgCAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACAAAACCTTGCCAGATGGCAAACCg  >  2:548292/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                                        CGGTTATCCGGGCGGCGTACCGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACAAAACCTTGCCAGATGGCAAACCG  >  NC_000913/2014137‑2014407

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑