New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 1046001	NA (NA)	8 (0.740)	8/166	0.3	66.7%	intergenic (+15/+418)	BW25113_RS05135/cspH	IS1‑like element IS1D family transposase/cold shock‑like protein CspH
	?	NZ_CP009273	= 1903046	4 (0.370)					intergenic (‑23/‑136)	mgrB/yobH	PhoP/PhoQ regulator MgrB/YobH family protein

GCCCAAAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCG  >  NZ_CP009273/1902962‑1903122                                                                                     |                                                                             gcCCAAAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTggtaa                                                                         >  1:312209‑M2/1‑85 (MQ=255)            caagcaagCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTggtaatgactccaact                                                              <  2:175945‑M2/90‑17 (MQ=255)                     cAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTggtaatgactccaacttattgatag                                                     >  1:83080‑M2/1‑65 (MQ=255)                            acGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTggtaatgactccaacttattgatagtgtttta                                              <  2:180572‑M2/90‑33 (MQ=255)                              ctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAg                                            <  2:10234‑M2/43‑1 (MQ=255)                                      gAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTggtaatgactccaacttattgatagtgttttatgttcagata                                    >  1:129801‑M2/1‑48 (MQ=255)                                        ccatcatccactaaatcagtaagttggcagcatcaccCACCTACCCTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTa                                  <  1:175945‑M2/53‑1 (MQ=255)                                        aCGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTggtaatgactccaacttattgatagtgttttatgttcagataat                                  >  2:154097‑M2/1‑46 (MQ=255)                                           aCCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGt                               >  1:143208/1‑90 (MQ=255)                                           aCCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGt                               >  1:222572/1‑90 (MQ=255)                                                tCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTa                                  >  1:188365/1‑82 (MQ=255)                                                tCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTa                                  <  2:188365/82‑1 (MQ=255)                                                          gtaagttggcagcatcaccCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATg                                <  1:292353‑M2/55‑1 (MQ=255)                                                          gtaagttggcagcatcaccCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATg                                >  2:292353‑M2/20‑74 (MQ=255)                                                                    agcatcaccCACCTACCTTATGTCATTAGACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGa      >  2:113893‑M2/10‑90 (MQ=255)                                                                     ctcCGTTTCACCTACCTggtaatgactccaacttattgatagtgttttatgttcagataatgcccgatgactttgtcatgcagctccacc     >  1:134398‑M2/1‑17 (MQ=255)                                                                        cGTTTCACCTACCTggtaatgactccaacttattgatagtgttttatgttcagataatgcccgatgactttgtcatgcagctccaccgat  <  2:299619‑M2/90‑77 (MQ=255)                                                                                     |                                                                             GCCCAAAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCG  >  NZ_CP009273/1902962‑1903122

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ 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.