Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC JC	CP009273	2,400,257	IS5 (+) +4 bp	50.0%	intergenic (‑137/‑780)	lrhA ← / → alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 2283592	NA (NA)	11 (0.620)	8/276	NT	54.3%	noncoding (1/1195 nt)	IS5	repeat region
	?	CP009273	= 2400260	9 (0.520)					intergenic (‑140/‑780)	lrhA/alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
*	?	CP009273	2400257 =	9 (0.520)	7 (0.410)	7/268	NT	43.8%	intergenic (‑137/‑783)	lrhA/alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
	?	CP009273	3358915 =	NA (NA)					noncoding (1195/1195 nt)	IS5	repeat region

TTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP009273/2283464‑2283592 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TTAGTGCAACTCATATGCATTTTTACTTTCGTCCGGGTTCCGGATGAAACTGCCAGGGAGGCACATTACAAATGGAATTGCTTGTTTGTGTGTGCACAGCATTAACCAGCTCAGTATGAGCCGC  <  CP009273/2400260‑2400137                                                                                                                                                                                                                                                               TTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCGTTAGTGCAGCTCATATGCAT                                                                                                          >  2:64090/1‑149          GACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTGCAACTCATATGCATTTTTACTTT                                                                                                 >  2:109087/1‑149                      TGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGAGAAACATGATCTCATATCGGGGACTTGTTCGCACCTTCCTTAGTGCAACTCATATGCATTTTTACTTTGGTCCGGGTTCg                                                                                     >  2:12983/1‑148                        CTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTGCAACTCATATGCATTTTTACTTTCGTCCGGGTTCCGG                                                                                   >  2:283253/1‑149                        CTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTGCAACTCATATGCATTTTTACTTTCGTCCGGGTTCCGG                                                                                   >  2:8521/1‑149                                      GGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACGTTCCTTAGTGCAACTCATATGCATTTTTACTTTCGTCCGGGTTCCGGATGAAACGGCGAGG                                                                     >  1:149119/1‑149                                      GGCGAAGGTAAGTTGATGACTCATGATGAACCATGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTGCAACTCATATGCATTTTTACTTTCGTCCGGGTTCCGGATGAAACTGCCAGG                                                                     >  1:149234/1‑149                                            gggAAGTTGATGACCCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTGCAACTCATATGCATTTTTACTTTCGTCCGGGTTCCGGATGAAACTGCCAGGGAGGCA                                                               <  1:311058/146‑1                                                             tcaacaaaaccggTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTGCAACTCATATGCATTTTTACTTTCGTCCGGGTTCCGGATGAAACTGCCAGGGAGGCACATTACAAATGGAATTG                                              >  1:53677/14‑149                                                                        GTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTGCAACTCATATGCATTTTTACTTTCGTCCGGGTTCCGGATGAAACTGCCAGGGAGGCACATTACAAATGGAATTGCTTGTTTGTGT                                   >  2:132197/1‑149                                                                                                         TATCAGGGACTTGTTCGCGCCTTCCTTAGTGCAACTCATATGCATTTTTACTTTCGTCCGGGTTCCGGATGAAACTGCCAGGGAGGCACATTACAAATGGAATTGCGTGTTTGTGTGTGCACAGCATTAACCAGCTCAGTATGAGCCGC  >  1:152407/1‑149                                                                                                                                                                                                                                                               TTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP009273/2283464‑2283592 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TTAGTGCAACTCATATGCATTTTTACTTTCGTCCGGGTTCCGGATGAAACTGCCAGGGAGGCACATTACAAATGGAATTGCTTGTTTGTGTGTGCACAGCATTAACCAGCTCAGTATGAGCCGC  <  CP009273/2400260‑2400137

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.