Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	2,737,118	IS1 (+) +8 bp	intergenic (+235/‑29)	bamD → / → raiA	outer membrane protein assembly factor BamD/stationary phase translation inhibitor and ribosome stability factor

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1978503 =	NA (NA)	31 (0.940)	23/160	0.4	100%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	2737118 =	0 (0.000)					intergenic (+235/‑36)	bamD/raiA	outer membrane protein assembly factor BamD/stationary phase translation inhibitor and ribosome stability factor
*	?	NC_000913	= 1979270	NA (NA)	23 (0.700)	19/160	0.7	100%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	= 2737125	0 (0.000)					intergenic (+242/‑29)	bamD/raiA	outer membrane protein assembly factor BamD/stationary phase translation inhibitor and ribosome stability factor

ATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTT  >  NC_000913/1978425‑1978581                                                                               |                                                                               aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATggg                                                                               >  2:352590/1‑80 (MQ=255)        ggAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACt                                                                       >  2:352604/1‑81 (MQ=255)           ggggggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTcc                                                                     >  2:352577/1‑80 (MQ=255)              gggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACt                                                                 >  2:352609/1‑81 (MQ=255)                      aTTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGa                                                           >  2:352586/1‑79 (MQ=255)                        tttCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAgt                                                       >  1:352607/1‑81 (MQ=255)                           cAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGtt                                                    >  2:352591/1‑81 (MQ=255)                             ataatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGtttt                                                  <  2:352569/81‑1 (MQ=255)                                  gCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAACTGCGTAATGACTCCAACTCATTGATAGTGTTTTATGtt                                             >  2:352605/1‑81 (MQ=37)                                   cGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGtt                                             >  1:352601/1‑80 (MQ=255)                                       aTGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGa                                         >  2:352608/1‑80 (MQ=255)                                          cAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCTACTTATTGATAGTGTTTTATGTTCAGATAAt                                     >  2:352583/1‑81 (MQ=255)                                            gATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGc                                   >  1:352598/1‑81 (MQ=255)                                             aTCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGcc                                  >  2:352597/1‑81 (MQ=255)                                                    aaaaCACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGAc                           <  1:352570/81‑1 (MQ=255)                                                      aaCACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACtt                         <  1:352571/81‑1 (MQ=255)                                                       acacTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACttt                        >  2:352610/1‑81 (MQ=255)                                                              aTTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGc                 <  2:352572/81‑1 (MQ=255)                                                                        aTAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCg       <  2:352573/81‑1 (MQ=39)                                                                             tGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGAtttt  >  1:352619/1‑81 (MQ=32)                                                                               |                                                                               ATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTT  >  NC_000913/1978425‑1978581

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ 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.