Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	248,419	A→G	pseudogene (1652/1713 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	248,419	0	A	G	100.0%	139.1 / NA	39	pseudogene (1652/1713 nt)	lfhA	flagellar system protein, promoterless fragment
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (27/12);  total (27/12)

ACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCACATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCACCGGGTC‑TTTCCCCGCCGCTTTCATCTGCTCTTTCACCTGTGGCATCGTACTCTGGAACTGGT  >  NC_000913/248282‑248554                                                                                                                                          |                                                                                                                                         aCAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGcgca                                                                                                                                        >  1:350838/1‑140 (MQ=255)  cAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCAt                                                                                                                                       >  1:104948/1‑140 (MQ=255)        tgtgCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGcc                                                                                                                                 <  2:826903/140‑1 (MQ=255)           gCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCg                                                                                                                              <  2:92271/140‑1 (MQ=255)                      aGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAaacaac                                                                                                                   >  2:522785/1‑140 (MQ=255)                             aTAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAaacaa                                                                                                                    <  2:19328/132‑1 (MQ=255)                             aTAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAaacaa                                                                                                                    >  1:19328/1‑132 (MQ=255)                             aTAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCAt                                                                                                            >  2:259691/1‑140 (MQ=255)                                 ggCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCaaa                                                                                                                       >  2:959265/1‑125 (MQ=255)                                 ggCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCaaa                                                                                                                       <  1:959265/125‑1 (MQ=255)                                     ttCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGcc                                                                                                    >  1:637874/1‑140 (MQ=255)                                      tCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTACAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATaa                                                                                                          >  2:230566/1‑133 (MQ=255)                                      tCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTACAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATaa                                                                                                          <  1:230566/133‑1 (MQ=255)                                         cgccgcATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCa                                                                                                <  1:259691/140‑1 (MQ=255)                                         cgccgcATCCGGCAGTTGTGCACCAATGCTGGATACGTACTTCAACGCTCCCATAATCTTCAACGCCAGCTCATCCGACTCTTCTTTACACGACAGCGCATGCAGCCCCTGCGCAAACAACCTTGCATAACGCGCCAGCa                                                                                                <  2:34012/140‑1 (MQ=255)                                              cATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAggg                                                                                           <  1:804705/140‑1 (MQ=255)                                               aTCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGgc                                                                                          <  1:267778/140‑1 (MQ=255)                                                tCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAggg                                                                                           <  1:969329/138‑1 (MQ=255)                                                tCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAggg                                                                                           >  2:969329/1‑138 (MQ=255)                                                          gtgCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGt                                                                               >  1:754598/1‑140 (MQ=255)                                                           tgCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTg                                                                              >  1:558734/1‑140 (MQ=255)                                                                  aTGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGc                                                                                     >  1:194864/1‑126 (MQ=255)                                                                  aTGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGc                                                                                     <  2:194864/126‑1 (MQ=255)                                                                  aTGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACcag                                                                       >  2:520088/1‑140 (MQ=255)                                                                        gATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCAc                                                                 <  2:462594/140‑1 (MQ=255)                                                                             ttACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCACCGGGt                                                            >  1:925380/1‑140 (MQ=255)                                                                             ttACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCAAGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCACCGGGt                                                            >  2:718488/1‑140 (MQ=255)                                                                              tACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCACCGGGTc                                                           >  1:807953/1‑140 (MQ=255)                                                                                     aCGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCACCGGGTC‑TTTcccc                                                   >  1:863933/1‑140 (MQ=255)                                                                                      cGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCACCGGGTC‑TTTCCccg                                                  >  2:625682/1‑140 (MQ=255)                                                                                      cGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCACCGGGTC‑TTTCCccg                                                  >  2:982007/1‑140 (MQ=255)                                                                                         ccccATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCACCGGGTC‑TTTCCccgccg                                               >  2:15602/1‑140 (MQ=255)                                                                                                  cTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCACCGGGTC‑TTTCCCCGCCGCTTTCATCt                                      <  1:982007/140‑1 (MQ=255)                                                                                                   tccaccTCCAGCTCACCCGGCTCTTCTTTATACGACAGCGCATGCAGCCCCGGCGCAAACACCCTTGCATACCGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCCCCGGGTC‑TTTCCCCGCCGCTTTCATCTg                                     <  2:925380/135‑1 (MQ=255)                                                                                                           cAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCACCGGGTC‑TTTCCCCGCCGCTTTCATCTGCTCTTTCa                             >  2:788435/1‑140 (MQ=255)                                                                                                           cAGCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCACCGGGTC‑TTTCCCCGCCGCTTTCATCTGCTCTTTCa                             >  1:429321/1‑140 (MQ=255)                                                                                                             gCTCATCCGGCACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCACCGGGTC‑TTTCCCCGCCGCTTTCATCTGCTCTTTCAcc                           >  2:132645/1‑140 (MQ=255)                                                                                                                    cGGCTCTTCGTTATACGACAGCGCAGGCAGCCCCGGCGCAAACACCTTTGCATACCGCGCCAGCAAGGGGCGCGGCTGCGGGGGCACCAGCAGCCCCGGGTT‑TTCCCCCGCCGCTTTCATCTGCTCTTTCACCTGTGGCa                    <  2:1017879/140‑1 (MQ=255)                                                                                                                       cctttCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGAATACCGCGCCAGCAAGGGGCGCAGCTGGGGTGGCACCAGCAGCACCGGGTC‑TTCCCCCGCCGCTTTCATCTGCTCTTTCACCTGTGGCATCg                 <  2:104948/137‑1 (MQ=255)                                                                                                                       cACTTCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCACCGGGTC‑TTTCCCCGCCGCTTTCATCTGCTCTTTCACCTGTGGCATCg                 >  1:1017879/1‑140 (MQ=255)                                                                                                                          ttCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCCCCGGGTC‑TTTCCCCGCCGCTTTCATCTGCTCTTTCACCTGTGGCATCGTAc              <  2:637874/140‑1 (MQ=255)                                                                                                                           tCGTTATACGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCACCGGGTC‑TTTCCCCGCCGCTTTCATCTGCTCTTTCACCTGTGGCATCGTAct             >  1:122895/1‑140 (MQ=255)                                                                                                                               tctaCGAGAGCAAATGCCGCCCGGGCGCAAACACCCTTCAAAAACCCGAGCGAAAGGGGGGCGGCTGGGGTGACACCAGCAGCCCGGGTTC‑TTCCCCCGCCGCTTTCATCTGCTCTTTCACCTGTGGCATCGTACTCTgg         <  2:344575/138‑1 (MQ=255)                                                                                                                               tataCGACAGCGCATGCAGCCCCGGCGAAAACAACCTTGAATACCGCGCAAGAAAGGGGCGCGGCGGCGGTGGCACCAGCAGC‑GCGGGTCTTTTCCCCGCCGCTTTCATCTGCTCTTTCACCTGTGGCATCGTACTCTgg         <  2:118849/140‑1 (MQ=255)                                                                                                                                   cGACAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCACCGGGTC‑TTTCCCCGCCGCTTTCATCTGCTCTTTCACCTGTGGCATCGTACTCTGGAACt     >  1:85885/1‑140 (MQ=255)                                                                                                                                      cAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCACCGGGTC‑TTTCCCCGCCGCTTTCATCTGCTCTTTCACCTGTGGCATCGTACTCTGGAACTGGt  >  1:344575/1‑140 (MQ=255)                                                                                                                                      cAGCGCATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCACCGGGTC‑TTTCCCCGCCGCTTTCATCTGCTCTTTCACCTGTGGCATCGTACTCTGGAACTGGt  >  1:118849/1‑140 (MQ=255)                                                                                                                                          |                                                                                                                                         ACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCGGCACTTCGTTATACGACAGCACATGCAGCCCCGGCGCAAACAACCTTGCATAACGCGCCAGCAAAGGGCGCAGCTGCGGTGGCACCAGCAGCACCGGGTC‑TTTCCCCGCCGCTTTCATCTGCTCTTTCACCTGTGGCATCGTACTCTGGAACTGGT  >  NC_000913/248282‑248554

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑