Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	2,666,074	IS1 (+) +9 bp	coding (640‑648/1281 nt)	csiE →	stationary phase‑inducible protein CsiE

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	279163 =	NA (NA)	7 (0.540)	6/290	0.5	100%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	2666074 =	0 (0.000)					coding (640/1281 nt)	csiE	stationary phase‑inducible protein CsiE
*	?	NC_000913	= 291401	NA (NA)	21 (1.620)	18/288	0.0	100%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	= 2666082	0 (0.000)					coding (648/1281 nt)	csiE	stationary phase‑inducible protein CsiE

GCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGACTGGCGAAGGCGTGGCTGGCCGAGTACACACCGCAAATCAAGTCGTTGAAAGATGAGCGTAA  >  NC_000913/291242‑291639                                                                                                                                                                |                                                                                                                                                                                                                                               ncAGTGAGAGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTgg                                                                                                                                                      >  1:64000/2‑250 (MQ=255)                                  aGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTgg                                                                                                                    <  1:7725/251‑1 (MQ=255)                                   gTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACAAAATCAGTAAGTTGGCAGCATCACCGAAGTTGCAGCCCGGATGTTTCACGTACCGATGGCGAATATCTGGCCTATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTg                                                                                                                     <  1:316625/249‑1 (MQ=255)                                   gTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACAGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCGATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGc                                                                                                                                                  <  1:324093/220‑1 (MQ=255)                                           gCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGaa                                                                                                                                                                                                          <  1:10245/156‑1 (MQ=255)                                              gTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATATGGAAGCAATc                                                                                                                                              <  1:176963/213‑1 (MQ=255)                                                                                                cAGAAGCCACTAGAGCACCTCAAAAACACCATCATACACGAAAGCAGTAAGTTGGCATGATCACCGAATTGTCAGCCCGGATGTTTCACGTACCTATGTCGAATAGCTGGCCGAGAAGGTTGCGGATCGATAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCgn                                                                                                                          <  1:41050/183‑2 (MQ=38)                                                                                                        aCTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGt                                                                                                                                                                                                                      <  1:182206/83‑1 (MQ=255)                                                                                                        aCTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCgg                                                                                                                                                                                    >  1:162290/1‑117 (MQ=255)                                                                                                           gnAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGACTGGCAAAGGCGTGGCTGGcc                                           >  1:255856/1‑251 (MQ=255)                                                                                                                  cTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGCTCGAGCAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGc                                                                                                                                      >  1:319054/1‑153 (MQ=255)                                                                                                                                           tCAGTAAGTTGGCAGCATCACCGAATTTTCCGCCCGGATGTTTCACGTACGTATGTCGACTATCTGGCCGATAAGGTTGAGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGATCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGACTGGCGAAGGCGTGGCTGGCCGAGTACACACCGCAAATCAAGTCGTTGaa              >  1:121174/1‑248 (MQ=255)                                                                                                                                               tAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGCTAAGGTTGCGGATCGAGAAGANNATGCagn                                                                                                                                                                 >  2:19292/1‑96 (MQ=255)                                                                                                                                                aaGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGACTGGCGAAGGCGTGGCTGGCCGAGTACACACCGCAAATCAAGTCGTTGAAAGATGAGc      <  1:19292/251‑1 (MQ=255)                                                                                                                                                  gTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCCCGTCCCTATGTCGACTATCTGGcagct                                                                                                                                                                                              >  1:323993/1‑61 (MQ=255)                                                                                                                                                      gcagcaTCACCGAATTTTCAGCCCGGATGTTTCACGTACCTCTGTCGAATATATGGCCGATAAGGTTGCGGATCGCGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGACTGGCGAAGGCGTGGCTGGCCGAGTACACACCGCAAATCAAGTCGTTGAAAGATGAGCGTaa  >  1:180461/1‑249 (MQ=255)                                                                                                                                                       nagcaTCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGACTGGCGAAGGCGTGGCTGGCCGAGTACACACCGCAAATCAAGTCGTTGAAAGATGAGCGTaa  >  1:38545/2‑248 (MQ=255)                                                                                                                                                              aCCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCAGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATATGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGAc                                                               >  1:140067/1‑180 (MQ=255)                                                                                                                                                                |                                                                                                                                                                                                                                               GCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGACTGGCGAAGGCGTGGCTGGCCGAGTACACACCGCAAATCAAGTCGTTGAAAGATGAGCGTAA  >  NC_000913/291242‑291639

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ 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.