Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	2,016,437	Δ2 bp :: IS186 (–) +8 bp :: Δ1 bp	coding (570‑577/687 nt)	fliH →	flagellar biosynthesis protein FliH

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2016437 =	0 (0.000)	60 (1.320)	55/478	0.0	100%	coding (570/687 nt)	fliH	flagellar biosynthesis protein FliH
	?	NC_000913	2514274 =	NA (NA)					noncoding (2/1345 nt)	IS186	repeat region
*	?	NC_000913	= 2016444	0 (0.000)	57 (1.250)	52/480	0.1	100%	coding (577/687 nt)	fliH	flagellar biosynthesis protein FliH
	?	NC_000913	= 2515615	NA (NA)					noncoding (1343/1345 nt)	IS186	repeat region

GAAAATTGCTTCCACGCTCTCTCCGCGTGCTGAAGGCATCATCTCTGTGTTCCTGGTTTCCTTCGCTAACTTCTCTTCAATCGGGATTATCGCAGGTGCAGTTAAAGGCCTGAATGAAGAGCAAGGTAACGTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCTCTAACCCGCCGCCGCGAAATTCGTGATGCTGCAACTCTGCTACGTCTGGGGCTGGCTTACGGCCCCGGGGGGATGTCATTACGTGAAGTCACTGCATGGGC  >  NC_000913/2514028‑2514521                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                        gAAAATTGCTTCCACGCTCTCTCCGCGTGCTGAAGGCATCATCTCTGTGTTCCTGGTTTCCTTCGCTAACTTCTCTTCAATCGGGATTATCGCAGGTGCAGTTAAAGGCCTGAATGAAGAGCAAGGTAACGTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTTGTGAGGGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCAt                                                                                                                                                                                                                                                     <  1:449346/251‑1 (MQ=255)            ccACGCTCTCTCCGCGTGCTGAAGGCATCATCTCTGTGTTCCTGGTTTCCTTCGCTAACTTCTCTTCAATCGGGATTATCGCAGGTGCAGTTAAAGGCCTGAATGAAGAGCAAGGTAACGTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGTCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCGGTAATACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAAc                                                                                                                                                                                                                                           <  1:23457/250‑1 (MQ=255)                     ctcCGCGTGCTGAAGGCATCATCTCTGTGTTCCTGGTTTCCTTCGCTAACTTCTCTTCAATCGGGATTATCGCAGGTGCAGTTAAAGGCCTGAATGAAGAGCAAGGTAACGTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATGAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAggg                                                                                                                                                                                                                                    <  1:400942/248‑1 (MQ=255)                       ccGCGTGCTGAAGGCATCATCTCTGTGTTCCTGGTTTCCTTCGCTAACTTCTCTTCAATCGGGATTATCGCAGGTGCAGTTAAAGGCCTGAATGAAGAGCAAGGTAACGTGGTTTCTCGCTTCGGTCTGAAGCTTGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGtt                                                                                                                                                                                                                                  <  2:310917/248‑1 (MQ=255)                              cTGAAGGCATCATCTCTGTGTTCCTGGTTTCCTTCGCTCACTTATCTTCAATCGGGATTATCGCAGGAGCAGTTAAAGGCCTGAATGAAGAGCACGGTAACGTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTAc                                                                                                                                                                                                                        >  1:307489/1‑251 (MQ=255)                                   ggCATCATCTCTGTGTTCCTTGTTTCCTTCGCTAACTTCTCTTCAATCGGGATTATCGCCGGTGCAGTTAAAGGCCTGAATGAAGAGCAAGGTAACTTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTTTGCTGTCTGCGTCAAGCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAAGGTTGTGGTATTACGCCTg                                                                                                                                                                                                                   <  2:307489/251‑1 (MQ=255)                                   ggCATCATCTCTGTGGTCCTGGTTTCCTTCGCTAACTTCTCTTCAATCGGGATTATCGCAGGTGCAGTTAAAGGCCTGAATGAAGAGCAAGGTAACGTGGTTTCGCGCTTCGGTCTGAAGCTGGTTTACGGCTCTGCCCTGGTGAGTGTGCTGTCTGCGTCGATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGAGAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTGTTACGCCTg                                                                                                                                                                                                                   <  2:198594/251‑1 (MQ=255)                                               gtgtTCCTGGTTTCCTTCGCTAACTTCTCTTCAATCGGGATTATCGCAGGTGCAGTTAAAGGCCTGAATGAAGAGCAAGGTAACGTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAAc                                                                                                                                                                                                       <  1:41318/251‑1 (MQ=255)                                                 gtTCCTGGTTTCCTTCGCTAACTTCTCTTCAATCGGGATTATCGCAGGTGCAGTTAAAGGCCTGAATGAAGAGCAAGGTAACGTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGt                                                                                                                                                                                                     <  1:173699/251‑1 (MQ=255)                                                   tCCTGGTTTCCTTCGCTAACTTCTCTTCAATCGGGATTATCGCAGGTGCAGTTAAAGGCCTGAATGAAGAGCAAGGTAACGTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGc                                                                                                                                                                                                   >  1:408185/1‑251 (MQ=255)                                                                 gCTAACTGCTCTTCAATCGGGATGATCGCAGGTGCAGTTAAAGGCCTGAATTAAGAGCAATGTAACGTGTTTTCTCGCTTCTGTCTGAAGCTGGTTTACGGCTCTACCCGGGTGAGTGTGCTGTCTGCGTCAATCGCTGCACGGGTTCTGTAAGACCATACATAAAAAAGCCGGGGATAATGCCCATAAGCGCGAACGTAAGGGTGGTGGTATTTCGCGTGATGTGATTTAACTTGCCGATGAATGActct                                                                                                                                                                                     <  2:244825/251‑1 (MQ=255)                                                                                                  gCAGTTAAAGGCCTGAATGAAGAGCAAGGTAACGTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCatat                                                                                                                                                     <  2:424794/250‑1 (MQ=255)                                                                                                           gtccTGAATGAATAGCAAGGTAACTTGGTTTCTCGCTTCGGTCTGAAGCGGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCGGCGTCAATCGCAGCACTGGTGCTGTAAGATCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGGGGTATTACGCCTGCTATTATTTAACGTGCTGAGGAATTACTCTCACTAGAACTGGTCAGCAATTCTGGTTCATATTGGTAAGccc                                                                                                                                           <  2:469595/249‑1 (MQ=255)                                                                                                                                                  ggTCTGACGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGCGCTGTCAGACCCTACATAAAAAAGCCGGGGACAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCCCGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGctct                                                                                                     >  1:302375/1‑250 (MQ=255)                                                                                                                                                  ggTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGctct                                                                                                     >  2:361549/1‑250 (MQ=255)                                                                                                                                                       gAAGCTGGTTTACGGCTCTACCCTGGTTAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTTTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTTTGGTATTACGCCTGATATTATTGAACGTGCCGATGAATTACTCGCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCTCTAAcc                                                                                                 <  1:456500/249‑1 (MQ=255)                                                                                                                                                                 tACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTCAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCTCTAACCCGCCGCCGCGa                                                                                      <  1:111004/250‑1 (MQ=255)                                                                                                                                                                                  gAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCTCTAACCCGCCGCCGCGAAATTCGTGATGCTGCAAc                                                                    >  1:421023/1‑251 (MQ=255)                                                                                                                                                                                   aGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCTCTAACCCGCCGCCGCGAAATTCGTGATGCTGCAAct                                                                   <  1:55736/251‑1 (MQ=255)                                                                                                                                                                                               gCGTCAATCGCAGCCCTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAAATCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACtt                                                                                                                           <  1:334576/183‑1 (MQ=255)                                                                                                                                                                                               gCGTCAATCGCAGCACTGGTGCTGTAAGACAATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACtt                                                                                                                           >  2:334576/1‑183 (MQ=255)                                                                                                                                                                                                       cGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCTCTAACCCGCCGCCGCGAAATTCGTGATGCTGCAACTCTGCTACGTCTGGggctggc                                               <  1:295048/251‑1 (MQ=255)                                                                                                                                                                                                        gcagcaCTGGTGGTGTAAGACCATACATAAAAAAGCTGGGGATAATTCCCATAAGCGCTACCGTAAGGGTTGGGGTATGACGACTGATAATATTTAACGTGCCGATGAATTACTCTCACGATACCTGGTCCGCAATTCTGGTCCATATTGGTAAGCCCGAAGAACGGGATACTTCGGCACGCAATGCCGGGCCTCTAACCCGCCGCCGCTTAATGCGTGATGAGGCAACGCTGCTACGTCTGGggctggct                                              <  2:278475/251‑1 (MQ=14)                                                                                                                                                                                                                   gCTGTAAGACCATACCTAAAAAAGCCGGGGATAATTCCCATAAGCGCCAACTTTAGGGTTGTGGTATTACGCCTGCTATGCTTTAACGTGACGATGTATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCTCTAACCCGCCGCCGCGAAATTCGTGATGCTGAAACTCTGCTACGTCTGGGGCTGGCTTCCGGCCCCgg                                   >  1:290346/1‑251 (MQ=14)                                                                                                                                                                                                                             catacataAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCTCTAACCCGCCGCCGCGAAATTCGTGATGCTGCAACTCTGCTACGTCTGGGGCTGGCTTACGGCCCCGGGGGGATGTc                          >  1:252192/1‑250 (MQ=40)                                                                                                                                                                                                                                acataAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTTCCGATGAATTACTCTCTCGATAACTGGTGAGCAATTCTGTCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCTGTAACCCGCCTCCGTGAAATTCGTGATGCTGTTACTCTGCTACGTCTGGGGCTGGCTTACGGCCACGGGGGGATGTCAtt                       <  1:285623/250‑1 (MQ=14)                                                                                                                                                                                                                                acataAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCTCTAACCCGCCGCCGCGAAATTCGTGATGCTGCAACTCTGCTACGTCTGGGGCTGGCTTACGGCCCCGGGGGGATGTCATTa                      <  1:163131/251‑1 (MQ=38)                                                                                                                                                                                                                                   taAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCTCTAACCCGCCGCCGCGAAATTCGTGATGCTGCAACTCTGCTACGTCTGGGGCTGGCTTACGGCCCCGGGGGGATGTCATTACgg                   >  2:335124/1‑250 (MQ=37)                                                                                                                                                                                                                                    aaaaaaGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCTCTAACCCGCCGCCGCGAAATTCGTGATGCTGCAACTCTGCTACGTCTGGGGCTGGCTTACGGCCCCGGGGGGATGTCATTACGt                   <  1:67948/250‑1 (MQ=37)                                                                                                                                                                                                                                         aGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCTCTAACCCGCCGCCGCGAAATTCGTGATGCTGCAACTCTGCTACGTCTGGGGCTGGCTTACGGCCCCGGGGGGATGTCATTACGTGAAGTc             >  1:167533/1‑251 (MQ=34)                                                                                                                                                                                                                                           ccGGGGATAATTCCCCTAAGCGATAACTTAAGGGTTGTGGTATTACGCCTGATATGCTTTAACGTGCCGATGAATTACTCTCACGATAACTGGGCAGCAATTCTGGCCCTTATTGGTAAGCCCGAAAAACTCGATACTTAGGCACGTACTGCCGGCGATCTCACCAGCCGCCGCGACATTCGTGATGCTGCAACTCTCCTTCGTCTGGGGCTGGCTTACGGCCACGGGGGGGTGTCATTACTGGAAGTccc           >  2:12123/1‑249 (MQ=11)                                                                                                                                                                                                                                            cGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCTCTAACCCGCCGCCGCGAAATTCGTGATGCTGCAACTCTGCTACGTCTGGGGCTGGCTTACGGCCCCGGGGGGATGTCATTACGTGAAGTCACt          <  2:421023/251‑1 (MQ=33)                                                                                                                                                                                                                                                    aTTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATCTGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCTCTAACCCGCCGCCGCGAAATTCGTGATGCTGCAACTCTGCTACGTCTGGGGCTGGCTTACGGCCCCGGGGGGATGTCATTACGTGAAGTCACTGAATGGGc  >  1:45143/1‑251 (MQ=11)                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                        GAAAATTGCTTCCACGCTCTCTCCGCGTGCTGAAGGCATCATCTCTGTGTTCCTGGTTTCCTTCGCTAACTTCTCTTCAATCGGGATTATCGCAGGTGCAGTTAAAGGCCTGAATGAAGAGCAAGGTAACGTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCTCTAACCCGCCGCCGCGAAATTCGTGATGCTGCAACTCTGCTACGTCTGGGGCTGGCTTACGGCCCCGGGGGGATGTCATTACGTGAAGTCACTGCATGGGC  >  NC_000913/2514028‑2514521

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.