Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	2,319,850	IS2 (+) +5 bp	coding (23‑27/2850 nt)	rcsC ←	histidine kinase RcsC

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2068941 =	NA (NA)	41 (1.110)	39/492	0.1	100%	noncoding (1331/1331 nt)	IS2	repeat region
	?	NC_000913	2319850 =	0 (0.000)					coding (27/2850 nt)	rcsC	histidine kinase RcsC
*	?	NC_000913	= 2319854	0 (0.000)	21 (0.570)	20/492	0.9	100%	coding (23/2850 nt)	rcsC	histidine kinase RcsC
	?	NC_000913	= 2997691	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region

TACGCCAGAGAAATAACTGGCTGGCTGCTACACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAA  >  NC_000913/2997450‑2997934                                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                                    tACGCCAGAGAAATAACTGGCTGGCTGCTACACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGct                                                                                                                                                                                                                                             <  1:208276/250‑1 (MQ=32)          gaAATAACTGGCTGGCTGCTACACCATGTTGCCGGGCAACGAGGGAGACCGTCAGCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGGCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTTGTTGTCTGGAGAGTCAGGGGGCCAGTCTAATCTTGCTCTTttcttcg                                                                                                                                                                                                                                   <  2:43689/251‑2 (MQ=255)                    gctggctgCTACACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATc                                                                                                                                                                                                                         >  1:365849/1‑251 (MQ=40)                       ggctgCTTCACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCttt                                                                                                                                                                                                                      <  2:239418/251‑1 (MQ=255)                                       tGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGat                                                                                                                                                                                                      >  1:133967/1‑251 (MQ=255)                                           gggCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTAGCTTTGAAAGATTTGTAGGataaat                                                                                                                                                                                                  <  2:233150/251‑1 (MQ=255)                                             gCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaataa                                                                                                                                                                                                <  2:86325/251‑1 (MQ=255)                                                  gAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTa                                                                                                                                                                                           <  1:183950/251‑1 (MQ=255)                                                   aGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTaa                                                                                                                                                                                          <  1:250079/251‑1 (MQ=255)                                                       agaCCGTCATCCCCGGTGCAAAGCTCTGCTGAACAATTGCGATCGTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCACCAATGACTAGTCTAAAAACGAGTAGTAAGACTATCACTGATTGAAGGGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCGCTGTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGTATAAATAACATTAAGTaa                                                                                                                                                                                      <  1:191083/251‑1 (MQ=17)                                                            gTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCGGTGTGGTACGCCGTCTGCGTTTCTCCTGCACTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGATATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCg                                                                                                                                                                                 <  1:112215/251‑1 (MQ=255)                                                              cATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGc                                                                                                                                                                                <  1:293849/250‑1 (MQ=255)                                                               aTCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCAt                                                                                                                                                                              <  2:365849/251‑1 (MQ=255)                                                                   ccGGTTCAAAGCTCTGCTGAACAAGTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGc                                                                                                                                                                          <  2:148272/251‑1 (MQ=255)                                                                        tCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCACTAAGACATCAAGCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTATAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTtct                                                                                                                                                                      <  1:12696/250‑1 (MQ=255)                                                                                        cAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCttt                                                                                                                                                     >  2:197679/1‑251 (MQ=255)                                                                                                           tgtgGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGAt                                                                                                                                  >  2:271844/1‑251 (MQ=255)                                                                                                            gtgGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGAt                                                                                                                                  <  2:345273/250‑1 (MQ=255)                                                                                                                                                               ccAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTAt                                                                                <  2:230809/249‑1 (MQ=255)                                                                                                                                                                    gACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATGCAGGGTGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAATTAACATTAAGTAAATCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGTGATTCTCCCCCTAATTCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAggtgg                                                                         <  1:254196/251‑1 (MQ=255)                                                                                                                                                                           cTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAAcc                                                                  >  1:132852/1‑251 (MQ=255)                                                                                                                                                                                                   aCTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATcc                                           >  2:376479/1‑250 (MQ=255)                                                                                                                                                                                                       aTTTAAATGATATTGGTTGTCTGGAGATTCAGGGGGACAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCCGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGTGATTCTCCCCCTAAATCAAGCTTTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGtt                                       <  2:276918/250‑1 (MQ=255)                                                                                                                                                                                                        tttAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTc                                      >  1:205774/1‑250 (MQ=255)                                                                                                                                                                                                               gATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCGTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCTCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTTTCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCATTGACt                               <  1:166842/250‑1 (MQ=255)                                                                                                                                                                                                                     ggTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCtt                        <  1:155373/251‑1 (MQ=255)                                                                                                                                                                                                                                       ggggCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAgaga      <  1:80630/251‑1 (MQ=255)                                                                                                                                                                                                                                           ccAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACaaa  <  2:119531/251‑1 (MQ=255)                                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                                    TACGCCAGAGAAATAACTGGCTGGCTGCTACACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAA  >  NC_000913/2997450‑2997934

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 37 ≤ 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.