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)	22 (0.800)	21/490	0.4	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)	43 (1.560)	42/488	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

CCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGAT‑GTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGACTGGCGAAGGCGTGGCTGGCCGAGTACACACCGCAAATCAAGTCGTTGAAAGATGAGCGTAAAGAGGCCTATCG  >  NC_000913/291169‑291651                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                           ccATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGAT‑GTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATg                                                                                                                                                                                                                                          >  1:137369/1‑251 (MQ=37)            aTTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCTTGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGAT‑GTCCGGCAGTGCTTTTGGCGTTACGCACCACCCCGTCATTAGCTGAACAGGAGGGACAGCTTATAGAAACAGAAGCCACTAGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAATTTTCAGCGCGGTTGTTGCACGTAcc                                                                                                                                                                                                                               <  2:120511/251‑1 (MQ=11)                tCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGAT‑GTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTAt                                                                                                                                                                                                                            <  1:13059/250‑1 (MQ=255)                               gTTGAGAAGCGGTGTAAGTGAAGTGCAGTTTCCAGGGTTTACGGCAGTGAGAGAAGAGATAGCGCTGAT‑GTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGGCAGTAGCTGAACAGTGGGGACAGCTGAGAGAAACAGAAGCCACGGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCAAATGTTCAGCCCGGATGTTTCACGTACCTAGTTCGCATATCTggacg                                                                                                                                                                                                            <  2:172403/251‑4 (MQ=14)                                  gagaAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTAAGGCAGAGAGAGCAAAGATAACGCTGAT‑GTCCGGAAGTGATTTTGCCGTTACGCACCACCCCGGCCGTCACTGAACCGGAGGGACAGCTGATAGAAACAGAAGGGACTGGAGCACCTCAAAAACACCATCATACACTCAATAAGTAAGTCGGCAGCATCGCCGAATTATCAGCCCGGCTGTTTCAAGTAACTATGTTGCATATCTGGCCggtc                                                                                                                                                                                                         >  1:112112/1‑248 (MQ=14)                                            gtAAGTGAACTGCAGTTGCCATGTTTTACGGCAGGGAGAGCAGAGATAGCGCTGAT‑GTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCgg                                                                                                                                                                                                >  1:101829/1‑250 (MQ=255)                                                                aTGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGAT‑GTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAgg                                                                                                                                                                           <  1:143573/251‑1 (MQ=255)                                                                              tGAGAGCAGAGATAGCGCTGAT‑GTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGc                                                                                                                                                              >  2:53976/1‑250 (MQ=255)                                                                                agagCAGAGATAGCGCTGATTGTC‑GGCAGTGCTTTTGCCGTTACGCACCACACCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCAGCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAAt                                                                                                                                                           <  1:269346/251‑1 (MQ=255)                                                                                      gagaTAGCGCTGAT‑GTCCGGCAGTGCTTTTGCCGTGACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATGTTCAGCCCGGATGTGTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGGAGCAATCATGGa                                                                                                                                                     <  2:101829/251‑1 (MQ=255)                                                                                                                  gttGCCGTTACGCACCGCCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATTGAGGCTCGTGTTACCGTTGCTGGCATgg                                                                                                                           <  2:57400/249‑1 (MQ=255)                                                                                                                      acGTTACCCACCCCCCGGTCAGTATCTGAACAGGAGGGAAACCTGCTAGAACCAGAAGCCACTGGAGCACCTCAAAAACACCATAATCCACTAAATCCGTAAGTCGGCAGCATCACCGAATTTTCAGACCGGATGCTTCACGTACCTATGTAGCATATCTGGCCGATAAGGTTGCTGATCGAGTAGCATATGCAGAGGAATATCTGGACTCAATCAAGGAGGCTCGTGTTTCAGTTGCTGGCATGGGGc                                                                                                                        >  2:278613/2‑249 (MQ=16)                                                                                                                             gCACCACCCCGTCAGTAGCTGAACAGGTGGAACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGAATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTggggctgg                                                                                                               >  1:57257/1‑245 (MQ=255)                                                                                                                              caccacCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATggg                                                                                                              >  2:39351/1‑250 (MQ=255)                                                                                                                               cccaccCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAg                                                                                                             <  1:224690/250‑1 (MQ=255)                                                                                                                                          aGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCACTCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGAAGGAtt                                                                                                   >  2:236296/1‑250 (MQ=255)                                                                                                                                          aGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGAtt                                                                                                   >  1:8387/1‑250 (MQ=255)                                                                                                                                          aGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTa                                                                                                  <  1:218919/251‑1 (MQ=255)                                                                                                                                           gTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACGCCATCATACACTAAATCAGTAAGTTGGCAGCATCAATGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGAGGGAGAGGAATAGCTGGGAGCGAGCATGTAGGCTCGTGTTACCGTTGCTGGCAAGGGGCTGGTGATGGAGGTGCAGGAttgc                                                                                                 <  2:133469/251‑3 (MQ=25)                                                                                                                                                  aaCAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGGGATGGAGGTGCAGGATTACTTCGATg                                                                                          >  1:111330/1‑251 (MQ=255)                                                                                                                                                            aCAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCg                                                                                 >  1:33113/1‑250 (MQ=255)                                                                                                                                                               gCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAg                                                                             <  2:65240/251‑1 (MQ=255)                                                                                                                                                                    tAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGACTTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGACTgg                                                                        >  1:260691/1‑251 (MQ=255)                                                                                                                                                                           aGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGACTGGCGAAGGc                                                                 <  1:98494/251‑1 (MQ=255)                                                                                                                                                                                      gAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGACTGGCGAAGGCGTGGCTGGCCg                                                      <  1:217516/251‑1 (MQ=255)                                                                                                                                                                                                             acacTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGACTGGCGAAGGCGTGGCTGGCCGAGTACACACCGCAAATCAAGTCg                               >  1:5658/1‑251 (MQ=255)                                                                                                                                                                                                                  aaaTCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGACTGGCGAAGGCGTGGCTGGCCGAGTACACACCGCAAATCAAGTCGTTg                            <  1:53976/249‑1 (MQ=255)                                                                                                                                                                                                                    aTCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGCTAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGGGCAGGATTACTTCGATGGCGCGGCCGATAGACTGGCGAAGGCGTGGCTGGCCGAGGACACACCGCAAATCAAGTCGTTGaa                          >  2:81957/1‑249 (MQ=255)                                                                                                                                                                                                                          aaGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATTGCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGAAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCCGGTGAGGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGACTGGCGAAGGCGTGGCTGGCCTGGTACACACCGCAAATCAAGTCGTTGTAAGATGAg                   <  2:83566/250‑1 (MQ=255)                                                                                                                                                                                                                               ggCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGACTGGCGAAGGCGTGGCTGGCCGAGTACACACCGCAAATCAAGTCGTTGAAAGATGAGCGTaa              >  2:104336/1‑250 (MQ=255)                                                                                                                                                                                                                                       cACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGACTGGCGAAGGCGTGGCTGGCCGAGTACACACCGCAAATCAAGCCGTTGAAAGATGAGCGTAAAGAGGCCt      >  2:196911/1‑250 (MQ=255)                                                                                                                                                                                                                                          cGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGACTGGCGAAGGCGTGGCTGGCCGAGTACACACCGCAAATCAAGTCGTTGAAAGATGAGCGTAAAGAGGCCTATCg  >  1:192711/1‑251 (MQ=255)                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                           CCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGAT‑GTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCAGGATTACTTCGATGGCGAGGCCGATAGACTGGCGAAGGCGTGGCTGGCCGAGTACACACCGCAAATCAAGTCGTTGAAAGATGAGCGTAAAGAGGCCTATCG  >  NC_000913/291169‑291651

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ 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.