Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC	NZ_CP009273	1,613,496	(CTGGATATTACCGCG)1→2	coding (120/435 nt)	marR →	multiple antibiotic resistance transcriptional regulator MarR

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	1613480 =	1 (0.080)	12 (0.950)	9/164	0.3	89.0%	coding (104/435 nt)	marR	multiple antibiotic resistance transcriptional regulator MarR
	?	NZ_CP009273	= 1613494	2 (0.160)					coding (118/435 nt)	marR	multiple antibiotic resistance transcriptional regulator MarR

TGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCC  >  NZ_CP009273/1613403‑1613546                                                                              |                                                                   tGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTAc                                                        <  2:80462/90‑1 (MQ=255)        ttaatccatatggttaatcagaagaaagatcgcctgcttaacgagtatctgtctccgctggatattaccgCGCTGGATACTACCGCGGca                                                 >  1:324578‑M1/71‑90 (MQ=255)         taatccatatggttaatcagaagaaagatcgcctgcttaacgagtatctgtctccgctggatattaccgCGCTGGATATTACCGCGGcac                                                >  2:111411‑M1/70‑90 (MQ=255)           atccatatggttaatcagaagaaagatcgcctgcttaacgagtatctgtctccgctggatattaccgCGCTGGATATTACCGCGGCACAg                                              <  2:188080‑M1/23‑1 (MQ=255)                tacggttaatcagaagaaagatcgcctgcttaacgagtatctgtctccgctggatattaccgCGCTGGATATTACCGCGGCACAGTTTaa                                         <  2:343627‑M1/28‑1 (MQ=255)                 atggttaatcagaagaaagatcgcctgcttaacgagtatctgtctccgctggatattaccgCGCTGGATATTACCGCGGCACAGTTTAAg                                        <  1:139193‑M1/29‑1 (MQ=255)                      taatcagaagaaagatcgcctgcttaacgagtatctgtctccgctggatattaccgCGCTGGATATTACCGCGGCACAGTTTAAGGtgct                                   <  1:146122‑M1/34‑1 (MQ=255)                       ttAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGcgctggatactaccgcggca                                  >  1:324578‑M2/1‑70 (MQ=255)                       aatcagaagaaagatcgcctgcttaacgagtatctgtctccgctggatattaccgCGCTGGATATTACCGCGGCACAGTTTAAGGtgctc                                  >  2:341686‑M1/56‑90 (MQ=255)                       aatcagaagaaagatcgcctgcttaacgagtatctgtctccgctggatattaccgCGCTGGATATTACCGCGGCACAGTTTAAGGtgctc                                  >  2:296276‑M1/56‑90 (MQ=255)                        tAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGcgctggatattaccgcggcac                                 >  2:111411‑M2/1‑69 (MQ=255)                          aTCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGcgctggatattaccgcggcacag                               <  2:188080‑M2/90‑24 (MQ=255)                            gaagaaagatcgcctgcttaacgagtatctgtctccgctggatattaccgCGCTGGATATTACCGCGGcac                                                <  1:49669‑M1/21‑1 (MQ=255)                            gaagaaagatcgcctgcttaacgagtatctgtctccgctggatattaccgCGCTGGATATTACCGCGGcac                                                >  2:49669‑M1/51‑71 (MQ=255)                               tacGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGcgctggatattaccgcggcacagtttaa                          <  2:343627‑M2/90‑29 (MQ=255)                                atGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGcgctggatattaccgcggcacagtttaag                         <  1:139193‑M2/90‑30 (MQ=255)                                     tAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGcgctggatattaccgcggcacagtttaaggtgct                    <  1:146122‑M2/90‑35 (MQ=255)                                      aaTCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGcgctggatattaccgcggcacagtttaaggtgctc                   >  2:296276‑M2/1‑55 (MQ=255)                                      aaTCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGcgctggatattaccgcggcacagtttaaggtgctc                   >  2:341686‑M2/1‑55 (MQ=255)                                        cctgcttaacgagtatctgtctccgctggatattaccgCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTgcgc                 >  2:259952‑M1/39‑90 (MQ=255)                                        cctgcttaacgagtatctgtctccgctggatattaccgCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTgcgc                 >  2:140853‑M1/39‑90 (MQ=255)                                           gaagaaAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGcgctggatattaccgcggcac                                 <  1:49669‑M2/71‑22 (MQ=255)                                           gaagaaAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGcgctggatattaccgcggcac                                 >  2:49669‑M2/1‑50 (MQ=255)                                                       ccTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGcgctggatattaccgcggcacagtttaaggtgctctgctctatccgctgcgc  >  2:259952‑M2/1‑38 (MQ=255)                                                       ccTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGcgctggatattaccgcggcacagtttaaggtgctctgctctatccgctgcgc  >  2:140853‑M2/1‑38 (MQ=255)                                                                              |                                                                   TGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCC  >  NZ_CP009273/1613403‑1613546

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ 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.