New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	3496884 =	74 (0.890)	3 (0.040)	3/256	NT	3.8%	intergenic (+7/‑119)	nirD/nirC	nitrite reductase (NADH) small subunit/nitrite transporter
	?	NC_000913	3496909 =	80 (0.980)					intergenic (+32/‑94)	nirD/nirC	nitrite reductase (NADH) small subunit/nitrite transporter
Rejected: Frequency below/above cutoff threshold.

AAAACAAAAAATAAAACAAAAAGTTTAAAAAATGTCCTGCAATATACCGAAGATTATTACAGGACCATGCAAAAAGGGGAGGCATTGCGCCTCCCGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3496981‑3496884 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttTTTGCATGGTCCTGTAATAATCTTCGGTATATTGCAGGACATTTTTTAAACTTTTTGTTTTATTTTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTG  >  NC_000913/3496909‑3497051                                                                                                                                                                                                                                                   AAAACAAAAAATAAAACAAAAAGTTTAAAAAATGTCCTGCAATATACCGAAGATTATTACAGGACCATGCAAAAACGGGAGGCGCAATGCCTCCCCTTTTTGCATGGTCCTGTAATAATCTTCGGTATATTGCAGGACATTTTTTAAA                                                                                               <  2:262241/148‑1                                                                    TGCAAAAAGGGGAGGCATTGCGCCTCCCGTTTTTGCATGGTCCTGTAATAATCTTCGGTATATTGCAGGACATTTTTTAAACTTTTT                                                                                         >  5:98040/1‑87                                                                    TGCAAAAAGGGGAGGCATTGCGCCTCCCGTTTTTGCATGGTCCTGTAATAATCTTCGGTATATTGCAGGACATTTTTTAAACTTTTT                                                                                         <  6:98040/87‑1                                                                                              CCGTTTTTGCATGGTCCTGTAATAATCTTCGGTATATTGCAGGACATTTTTTAAACTTTTTGTTTTATTTTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTG  <  1:262241/148‑1                                                                                                                                                                                                                                                   AAAACAAAAAATAAAACAAAAAGTTTAAAAAATGTCCTGCAATATACCGAAGATTATTACAGGACCATGCAAAAAGGGGAGGCATTGCGCCTCCCGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3496981‑3496884 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttTTTGCATGGTCCTGTAATAATCTTCGGTATATTGCAGGACATTTTTTAAACTTTTTGTTTTATTTTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTG  >  NC_000913/3496909‑3497051

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.