Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	249,545	T→C	pseudogene (526/1713 nt)	lfhA ←	flagellar system protein, promoterless fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	249,545	0	T	C	100.0%	53.5 / NA	18	pseudogene (526/1713 nt)	lfhA	flagellar system protein, promoterless fragment
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (7/11);  total (7/11)

GATGGTGCGGGTCAGCGTTTCGAGGCTTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCATCCGCCAGCCGGTAAAACCAAGCAGGGCGCTGAACAGCAAAAACGGCAGGTGCGGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGA  >  NC_000913/249423‑249664                                                                                                                           |                                                                                                                        gATGGTGCGGGTCAGCGTTTCGAGGCTTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCATCCGCCAGCCGGTAAAACCAAGCAGGGCGATGAACAGCAAAAACGGCAGGTGCGGGGATCCCGGTatc                                                                                                               >  1:153654/1‑131 (MQ=255)          ggTCAGCGTTTCGAGGCTTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCATCCGCCAGCCGGTAAAACCAAGCAGGGCGCTGAACAGCAAAAACGGCAGGTGCGGCACTCCCGGTACCACCGCCAGc                                                                                                      >  1:332614/1‑133 (MQ=255)                     cGAGGCTTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCATCCGCCAGCCGGTAAAACCAAGCAGGGCGCTGAACAGCAAAAACGGGAGGGGCGGCACTCCCGAGACCACCCACAGCCCGAACATAAt                                                                                           >  2:224052/1‑133 (MQ=255)                        ggCTTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCATCCGCCAGCCGGTAAAACCAAGCAGGGCGCTGAACAGCAAAAACGGCAGGTGCGGCACTCCCGGTACCACCGCCAGCACGAACATAATccc                                                                                        <  2:332614/133‑1 (MQ=255)                             ttCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCATCCGCCAGCCGGTAAAACCAAGCAGGGCGCTGAACAGCAAAAACGGCAGGGGCGGCACTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTgg                                                                                   >  2:28445/1‑133 (MQ=255)                             ttCTCTTCCGCCTCCCCCACCAACGGCTGTCTGCTCATCCGCCAGCCGGTAAAACCAAGCAGGGCGCTGAACAGCAAAAACGGCAGGTGCGGCACTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTgg                                                                                   <  1:221292/133‑1 (MQ=255)                               ctctTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCATCCGCCAGCCGGTAAAACCAAGCAGGGCGCTGAACAGCAAAAACGGCAGGTGCGGCACTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCg                                                                                 <  2:41549/133‑1 (MQ=255)                                  tcccgcctgcgccGCCAGTGGCTGTTTGCTCATCCGCCAGCCGGTAAAACCAAGCAGGGCGCTGAACAGCAAAAACGGCAGGTGCGGCACTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGgtg                                                                              <  1:176483/131‑1 (MQ=255)                                                                 aTCCGCCAGCCGGTATAATCAATCAGGGCGCTGAACAGCAAAAACGGCAGGTGCGGCACTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGt                                               <  1:224052/133‑1 (MQ=255)                                                                 aTCCGCCAGCCGGTAAAACCAAGCAGGGCGCTGAACAGCAAAAACGGCAGGGGCGGCACTCCCGGTACCACCGCCCGCACGAACATAATCCCGGTGGCGGGGTAGAGCACCGACGGGGTTGCCAGCAGCTggg                                               >  2:105209/1‑132 (MQ=255)                                                                         gCCGGTAATACCAAGTAGTGCGATGAACAGTAAAAACGGCAGGTGCGGCACTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACg                                       <  1:292626/133‑1 (MQ=255)                                                                         gCCGGTAAAACCAAGCAGGGCGCTGAACAGCAAAAACGGCAGGTGCGGCACTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACg                                       <  1:80456/133‑1 (MQ=255)                                                                               aaaaCCAAGCAGGGCGCTGAACAGCAAAAACGGCAGGTGCGGCACTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATgg                                 >  2:437655/1‑133 (MQ=255)                                                                                       gCAGGGCGCTGAACAGCAAAAACGGCAGGTGCGGCACTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATc                         >  2:499996/1‑133 (MQ=255)                                                                                           ggCGCTGAACAGCAAAAACGGCAGGTGCGGCACTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCg                     >  1:406649/1‑133 (MQ=255)                                                                                                       cAAAAACGGCAGGTGCGGCCCTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGAcg         <  1:499996/133‑1 (MQ=255)                                                                                                       cAAAAACGGCAGGTGCGGCACTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGAcg         <  1:105209/133‑1 (MQ=255)                                                                                                       cAAAAACGGCAGGTGCGGCACTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGAcg         >  2:559534/1‑133 (MQ=255)                                                                                                         aaaaCGGCAGGTGCGGCACTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGAcgcg       <  1:437655/133‑1 (MQ=255)                                                                                                           aaCGGCAGGTGCGGCACTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCggg     <  2:329930/133‑1 (MQ=255)                                                                                                              ggCAGGTGCGGCACTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGa  >  2:622719/1‑133 (MQ=255)                                                                                                                           |                                                                                                                        GATGGTGCGGGTCAGCGTTTCGAGGCTTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCATCCGCCAGCCGGTAAAACCAAGCAGGGCGCTGAACAGCAAAAACGGCAGGTGCGGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGA  >  NC_000913/249423‑249664

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑