Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	AM260480	635,877	T→C	E259E (GAA→GAG)	fliM ←	flagellar motor switch protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AM260480	635,877	0	T	C	100.0%	137.8 / NA	36	E259E (GAA→GAG)	fliM	flagellar motor switch protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (19/17);  total (19/17)

GGGCACGCCGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACTTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTACGG  >  AM260480/635751‑635990                                                                                                                               |                                                                                                                  gggCACGCCGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCcg                                                                                                            <  1:1159233/134‑1 (MQ=255)       gCCGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCcgcgcg                                                                                                        >  1:346395/1‑132 (MQ=255)        ccGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAg                                                                                                     <  1:1102893/134‑1 (MQ=255)         cGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCcgcg                                                                                                          <  2:155292/128‑1 (MQ=255)         cGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCcgcg                                                                                                          >  1:155292/1‑128 (MQ=255)                 ttGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGa                                                                                            >  2:85925/1‑134 (MQ=255)                           ccTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGt                                                                                   >  1:425642/1‑133 (MQ=255)                              tctcCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGAcc                                                                               >  1:57785/1‑134 (MQ=255)                                tcCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGAcc                                                                               >  2:986046/1‑132 (MQ=255)                                       gCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTg                                                                      <  2:478961/134‑1 (MQ=255)                                               ggCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGActtc                                                              <  1:85925/134‑1 (MQ=255)                                                      cGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCg                                                       >  1:359965/1‑134 (MQ=255)                                                      cGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCg                                                       >  2:1144136/1‑134 (MQ=255)                                                                       gCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATtcat                                      <  2:346395/134‑1 (MQ=255)                                                                         cAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATtcatca                                    <  1:1144136/134‑1 (MQ=255)                                                                                       cGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGc                      <  1:550438/134‑1 (MQ=255)                                                                                        ggTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCg                     <  2:359965/134‑1 (MQ=255)                                                                                                gCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAg                                                                                                     <  1:595693/46‑1 (MQ=255)                                                                                                gCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAg                                                                                                     >  2:595693/1‑46 (MQ=255)                                                                                                  aGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTtct                                                         >  1:661701/1‑88 (MQ=255)                                                                                                  aGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTtct                                                         <  2:661701/88‑1 (MQ=255)                                                                                                     tGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTACTTGAGCGGCTCGATCATcgc        <  2:425642/134‑1 (MQ=255)                                                                                                        gcgAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCg                                                                                                <  1:597648/43‑1 (MQ=255)                                                                                                        gcgAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCg                                                                                                >  2:597648/1‑43 (MQ=255)                                                                                                        gcgAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGt                                                                                        <  2:1039689/51‑1 (MQ=255)                                                                                                        gcgAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGt                                                                                        >  1:1039689/1‑51 (MQ=255)                                                                                                        gcgAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGccc                                                                         >  2:754440/1‑66 (MQ=255)                                                                                                        gcgAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGccc                                                                         <  1:754440/66‑1 (MQ=255)                                                                                                        gcgAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCt                                                                        <  2:988938/67‑1 (MQ=255)                                                                                                        gcgAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCt                                                                        >  1:988938/1‑67 (MQ=255)                                                                                                        gcgAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTa     >  1:536014/1‑134 (MQ=255)                                                                                                          gAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGAc                                                                                <  2:1139974/57‑1 (MQ=255)                                                                                                          gAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGAc                                                                                >  1:1139974/1‑57 (MQ=255)                                                                                                          gAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGTGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTACg   >  1:781037/1‑134 (MQ=255)                                                                                                          gAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTACg   >  1:676093/1‑134 (MQ=255)                                                                                                           aaCTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTACgg  >  1:670083/1‑134 (MQ=255)                                                                                                                               |                                                                                                                  GGGCACGCCGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACTTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTACGG  >  AM260480/635751‑635990

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑