Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	2,406,780	IS1 (–) +8 bp	intergenic (‑139/‑774)	lrhA ← / → alaA	DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1978503 =	NA (NA)	96 (1.180)	65/596	0.1	100%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	= 2406787	0 (0.000)					intergenic (‑146/‑774)	lrhA/alaA	DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA
*	?	NC_000913	= 1979270	NA (NA)	71 (0.870)	56/598	0.3	100%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	2406780 =	0 (0.000)					intergenic (‑139/‑781)	lrhA/alaA	DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA

GTAAAATCGTGTTGAGGCCAACGCCCATAATGCGGGCTGTTGCCCGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCC  >  NC_000913/1978972‑1979271                                                                                                                                                                                                                                                                                                           |  gTAAAATCGTCTTGAGGCCAACCCCCACAATTCGGGTTGGTGTCCGGGATATAACGCCATCCATGGCCATCTCAAGAATTGTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAGCTGCAGTTGGCATGGTTTGCGGCAGTGAGAGCAGAGAGAGCGCTGATGTCCGGCGGTGCTTGTGCTGTTACGCACCACCCCGTCAGTAGCGGAAAAAGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAATTGGCAGCATCAccc  <  2:77177/300‑1 (MQ=11)                                                                                                                                                                                                                                                                                                           |  GTAAAATCGTGTTGAGGCCAACGCCCATAATGCGGGCTGTTGCCCGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCC  >  NC_000913/1978972‑1979271

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 40 ≤ 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.