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)	15 (1.480)	12/298	0.0	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)	10 (0.990)	9/296	0.1	100%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	= 2666082	0 (0.000)					coding (648/1281 nt)	csiE	stationary phase‑inducible protein CsiE

CTGACGGTGGTAATGGCGCGCACAAAGCTGTAAATCAGCGCCGAGAGGATCGCCGGGCGCAGCAGCGGCAGCAGGATGTGCGTAATGGTACGCAGGGAACCGGCGCGCAGGCTGAGTGAGGCTTCATCGAGCGATTTATCGATTTGGCCCGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCTGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATC  >  NC_000913/279013‑279388                                                                                                                                                       |                                                                                                                                                                                                                                  cTGACGGTGGTAATGGCGCGCACAAAGCTGTAAATCAGCGACGAGAGGATCGCCGGGCGCAGCAGCGGCAGAAGGATGTGCGTAATGGTACGCAGGGAACCGGCGCGCAGGCTGAGTGAGGCTTCATCGAGCGATTTATCGATTTGGCCCGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCTGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTc                                                                                                                               >  1:207729/1‑251 (MQ=255)                   cgcACAAAGCTGTAAATCAGCGCCGAGAGGATCGCCGGGCGCAGCAGCGGCAGCAGGATGTGCGTAATGGTGCGCAGGGAACCGGCGCGCAGGCTGAGTGAGGCTTCATCGAGCGATTTATCGATTTGGCCCGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCTGCTCCACCGATTTTGAGAACGAc                                                                                                                                            <  1:243149/220‑1 (MQ=255)                                 aaTCAGCGCCGAGAGGAGCGCCGGGCGCAGCAGCGGCAGCAGGATGTGCGTAATGGTACGCAGGGAACCGGCGCGCAGGCTGAGTGAGGCTTCATCGAGCGATGTATCGATTTGGCCCGGTAATGACTCCAACTGATTGATAGGGTTTTATGTTCAGATAACGCCCGATGACTTTGTCATGCGTCTCCACCGAGTTTGAGAACGACAGCGACTTCCGTCCCATTCGTGCTAAGTGCTGCCTCAGATTCAgg                                                                                               <  1:208745/251‑1 (MQ=25)                                               ggATCGCCGGGCGCAGCAGCGGCAGCAGGATGTGCGTAATGGTACGCAGGGAAACGCCGCAAAGCCTGTGTGAGGCTTCATAGAGAGATTTATCGATTTGGCCAGGTACTGAATCCCACTTCTTGCTAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCTGCTCCAACGATTTTGAAAACAACAGCACCTTCCGCCCCAGCCGAGCCAGGCGCTGCCTCAGATTAAGGATATGACGCTccat                                                                                 >  1:169678/1‑248 (MQ=16)                                                           ncagcagCGGCAGCAGGATGTGCGTAATGGTACGCAGGGAACCGGCGCGCAGGCTGAGTGAGGCTTCATCGAGCGATTTATCGATTTGGCCCGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCTGCTCCACCGATTTTGAGAACGACAGCGa                                                                                                                                       >  1:153385/2‑185 (MQ=255)                                                            cagcagCGGCAGCAGGATGTGCGTAATGGTACGCAGGGAACCGGCGCGCAGGCTGAGTGAGGCTTCATCGAGCGATTTATCGATTTGGCCCGGTAATGACTc                                                                                                                                                                                                                         <  1:6388/102‑1 (MQ=255)                                                              gcagcGGCAGCAGGATGTGCGTAATGGTACGCAGGGAACCGGCGCGCAGGCTGAGTGAGGCTTCATCGAGCGATTTATCGATTTGGCCCGGTAATGACTCCAACTTATTGATAGTGTTTTATGTACAGATAATGCCCGATGACTTTGtt                                                                                                                                                                        <  1:70713/149‑2 (MQ=255)                                                                 gcGGCAGCAGGATGTGCGTAATGGTACGCAGGGAACCGGCGCGCAGGCTGAGTGAGGCTTCATCGAGCGATTTATCGATTTGGCCCGGTAATGACTCCAAATTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCTGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCCGGTTATGCCGCTCAATTCGCTGCGTATATCGCtt                                                               >  1:114666/1‑251 (MQ=255)                                                                     cagcagGATGTGCGTAATGGTACGCAGGGAACCGGCGCGCAGGCTGAGTGAGGCTTCATCGAGCTATTTAGCGATTTGGCCCGGTAATGACTCCAACTTAGTGATAGTGTTTTATTTTCAGATAATGCCCGATGACTTTGTCATGCTGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTg                                                                                                                      <  1:81876/192‑1 (MQ=255)                                                                                         tACGCAGGGAACCGGCGCGCAGGCGGAGTGAGGCTTCATCGAGCGATTTATCGATTAGGTCCGGTAATGACTCCAACTTATTGATAGTGTTTTATGTCCAGATAATGCCCGATGACTTTGTCATGGTGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGc                                                                                                                          <  1:34263/168‑1 (MQ=18)                                                                                                           gcANGCTGAGTGAGGCTTCATCGAGCGATTTATCGATTTGGCCCGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAACGCCCGATGACGTTGTCATGCTGCTCCCCCGATTTTGAGAACGACAGcta                                                                                                                                       <  2:153385/137‑3 (MQ=21)                                                                                                              ggCTGAGTGAGGCTTCATCGAGCGATTTATCGATTTGGCCCGGTAATGACTCCAACTTATTGATAGTGTTTGATGTTCAGATAATGCCCGATGACTTTGTCATGCTGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGc                                                                                         <  1:80791/180‑1 (MQ=255)                                                                                                                         ncTTCATCGAGCGATTTATCGATTTGGCCCGGTAATGACTCAAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCTGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCg       >  1:155470/2‑251 (MQ=255)                                                                                                                              aTCGAGCGATTTATCGATTTGGCCCGGTAATGACTCCAACTTATTGATAGTGTGTTATGTTCAGATAATGCCCGATGACGTTGTCATGCTGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGTCTCAGATTCAGGTTATGCCGCTCAATTCGCGGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGTCGGGATTCATACAGCGGCCAGCCATCCGTCATc  <  1:110866/251‑1 (MQ=255)                                                                                                                                   gCGATTTATCGATTTGGCCCGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCTGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTg                                                                           >  1:9322/1‑173 (MQ=255)                                                                                                                                                  ggCCCGGTAATGACTCCAACTTATTGATAGTGTTTGATGGTCAGATAATGCCCGATGACTTTGTCATGCTGCGCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGTTGCGGCCTCAGATTCAGGTTATGCCGCTCAATTCGc                                                                             <  1:171644/156‑1 (MQ=11)                                                                                                                                                    cccGGGAATGACTCCAACTTACTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATTCTGCTCCACCGATTTTGAGAACGACAGCGACTTCCGGCCCAGCCGTGCCAGGTGCTGCCGCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGc                                                  <  1:110513/181‑1 (MQ=11)                                                                                                                                                     ccGGTAATGACTCCGACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCTGCTCCACCGATTTTGAGAACGACAGAGACTTACGTCCCAGCCGTGCCAGGTGCTGCCTCAGAATCANGTTNNNNNGcnnnnnn                                                                                >  2:150909/1‑144 (MQ=11)                                                                                                                                                       |                                                                                                                                                                                                                                  CTGACGGTGGTAATGGCGCGCACAAAGCTGTAAATCAGCGCCGAGAGGATCGCCGGGCGCAGCAGCGGCAGCAGGATGTGCGTAATGGTACGCAGGGAACCGGCGCGCAGGCTGAGTGAGGCTTCATCGAGCGATTTATCGATTTGGCCCGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCTGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATC  >  NC_000913/279013‑279388

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ 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.