New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	3583427 =	NA (NA)	10 (0.230)	8/276	NT	14.5%	intergenic (+10/‑55)	yrhA/insA	pseudogene, interrupted by IS1E/IS1 repressor TnpA
	?	NC_000913	3658812 =	59 (1.350)					coding (448/528 nt)	gadE	gad regulon transcriptional activator

GCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3583566‑3583427 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAGTCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACC  >  NC_000913/3658812‑3658958                                                                                                                                                                                                                                                                                                 GCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATACAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAGAAATTC                                                                                                                                            <  2:773375/149‑1          CGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAGAAATTCAACATTATG                                                                                                                                   <  1:592440/149‑1                                 ACCACCCCGCCACGAGGCTAACATGATGGACAGCTGATATAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCAGACACGAAGTCAGTAAGTTGGCAGCATCACCCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTAT                                                                                                            <  2:454171/149‑1                                            AGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCG                                                                                                 >  1:617223/1‑149                                                 CTGAACAGGAGGGACAGGTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATAATACACTAAATCAGTAAGTTGGCAGCATCACCCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACC                                                                                            >  2:578967/1‑149                                                     ACAGGACGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGG                                                                                        <  2:425328/149‑1                                                                                               TCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTATTCAGGACAAAACCAAATGAAAT                                              >  2:442120/1‑149                                                                                               TCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAGTCAGGCCATAAGCAACTGAAAT                                              >  2:742061/1‑149                                                                                               TCAAAAACACCATCATACACTAAATCAGTAAGTTGACAGCATCACCCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAGTCAGGACATAAGCAACTGCAAT                                              >  1:436968/1‑149                                                                                                                                  GCAGCATCACCCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAGTCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGAT           <  1:751490/149‑1                                                                                                                                           CCCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATAGTCACCCTGGGTATCACATCTTATTTTTAGTCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACC  <  1:578967/149‑1                                                                                                                                                                                                                                                                                                 GCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3583566‑3583427 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAGTCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACC  >  NC_000913/3658812‑3658958

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.