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)	24 (0.750)	21/160	0.6	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)	28 (0.880)	23/160	0.4	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

ACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAA  >  NC_000913/1979192‑1979350                                                                               |                                                                                 aCAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCa                                                                                <  2:361656/81‑1 (MQ=32)        aTAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGt                                                                         <  2:361657/81‑1 (MQ=255)           gAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGtata                                                                      <  1:361658/81‑1 (MQ=255)            aaaCAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGtat                                                                       >  1:361681/1‑79 (MQ=255)                  aaGACACTGGAGCACCTCAAAAACACCATAATACACTAGATCAGTAAGTTGGCAGCGTCACCCATAAATGTATAAGTCATa                                                               <  2:361659/81‑1 (MQ=18)                      cACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACttt                                                           <  2:566691/81‑1 (MQ=255)                          ggAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACttttgtt                                                       >  2:361688/1‑81 (MQ=255)                            aGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACttttgtttt                                                     <  2:361660/81‑1 (MQ=255)                            aGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACttttgtttt                                                     <  1:361661/81‑1 (MQ=255)                              cACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTgg                                                   <  1:361662/81‑1 (MQ=255)                               aCCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGCTTTggg                                                  >  1:361682/1‑81 (MQ=255)                                ccTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGgt                                                 <  1:361664/81‑1 (MQ=255)                                ccTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGgt                                                 <  2:361663/81‑1 (MQ=255)                                       aaCACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTc                                          <  1:361665/81‑1 (MQ=255)                                         cacCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCaa                                        >  2:361691/1‑81 (MQ=255)                                             atcatACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTg                                    <  1:361666/81‑1 (MQ=255)                                                atACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGtt                                  <  1:361667/80‑1 (MQ=255)                                                               aaGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgcta                  >  2:361692/1‑81 (MQ=255)                                                                        gcaTCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaa         <  1:361668/81‑1 (MQ=255)                                                                             aCCCATAAATGTATAAGTCATACTTTTTTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAgcaagcaa     <  2:361669/80‑1 (MQ=255)                                                                               ccATAAATGTATATGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa  >  2:361685/1‑81 (MQ=255)                                                                               |                                                                                 ACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAA  >  NC_000913/1979192‑1979350

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ 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.