New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 2405625	81 (0.750)	14 (0.140)	8/164	NT	15.8%	intergenic (‑553/+78)	nuoA/lrhA	NADH:ubiquinone oxidoreductase, membrane subunit A/transcriptional repressor of flagellar, motility and chemotaxis genes
	?	NC_000913	= 2405660	75 (0.750)					intergenic (‑588/+43)	nuoA/lrhA	NADH:ubiquinone oxidoreductase, membrane subunit A/transcriptional repressor of flagellar, motility and chemotaxis genes

TTTTTCAGGCGATTATTTGTGCGTTCGGGACGTGAATCTCTGGTGGTTGAAAAATGAACAGTTTTGTACGTTCTGCACTATGCGATGAAGGATTTTTACTAAAAAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/2405520‑2405625 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑taaaaaaCGAGCCGCTGGGGGTGTTTTAAACCCCAGCGGCTTTTTTTTAGTAAAAATCCTTCATCGCATAGTGCAGAACGTACAAAACTGTTCATTTTTCAA  <  NC_000913/2405660‑2405566                                                                                                                                                                                                           TTTTTCAGGCGATTATTTGTGCGTTCGGGACGTGAATCTCTGGTGGTTGAAAAATGAACAGTTTTGTACGTTCTGCACTATGCGATGAAGGATTTTTACT                                                                                                       <  2:403251/100‑1    TTCAGGCGATTATTTGTGCGTTCGGGACGTGAATCTCTGGTGGTTGAAAAATGAACAGTTTTGTACGTTCTGCACTATGCGATGAAGGATTTTTACTAAA                                                                                                    <  1:3019402/100‑1                                       TCTGGTGGTTGAAAAATGAACAGTTTTGTACGTTCTGCACTATGCGATGAAGGATTTTTACTAAAAAA‑AAGCCGCTGGGGGTGTTTTAAACCCCAGCGGC                                                                <  1:1359069/100‑1                                       TCTGGTGGTTGAAAAATGAACAGTTTTGTACGTTCTGCACTATGCGATGAAGGATTTTTACTAAAAAA‑AAGCCGCTGGGGGTGTTTTAAACCCCAGCGGC                                                                <  1:2984445/100‑1                                       TCTGGTGGTTGAAAAATGAACAGTTTTGTACGTTCTGCACTATGCGATGAAGGATTTTTACTAAAAAA‑AAGCCGCT‑GGGGTGTTTTAAACCCCAGCGGCT                                                               <  1:654765/100‑1                                        CTGGTTGTTGAAAAATGAACAGTTTTGTACGTTCTGCACTATGCGATGAAGGATTTTTACTAAAAAACGAGCCGCTGGGGGTGTTTTAAACCCCAGCGGC                                                                <  1:1303207/100‑1                                        CTGGTGGTTGAAAAATGAACTGTTTTGTACGTTCTGCAATATGCGATGAAGGATTTTTACTAAAAAA‑AAGCCGCTGGGGGTGTTTTAAACCCCAGCGGCT                                                               <  1:1217562/100‑1                                        CTGGTGGTTGAAAAATGAACAGTTTTGTACGTTCTGCACTATGCGATGAAGGATTTTTACTAAAAAACGAGCCGCTGGGGGTGTTTCAAACCCCAGCGGC                                                                <  1:2065116/100‑1                                        CTGGTGGTTGAAAAATGAACAGTTTTGTACGTTCTGCACTATGCGATGAAGGATTTTTACTAAAAAA‑AAGCCGCTGGGGGTGTTTTAAACCCCAGCGGCT                                                               <  1:3026056/100‑1                                        CTGGTGGTTGAAAAATGAACAGTTTTGTACGTTCTGCACTATGCGATGAAGGATTTTTACTAAAAAA‑AAGCCGCTGGGGGTGTTTTAAACCCCAGCGGCT                                                               <  1:907099/100‑1                                              GTTGAAAAATGAACAGTTTTGTACGTTCTGCACTATGCGATGAAGGATTTTTACTAAAAAA‑AAGCCGCTGGGGGTGTTTTAAACCCCAGCGGCTTTTTT                                                          <  2:2774788/99‑1                                                 GAAAAATGAACAGTTTTGTACGTTCTGCACTATGCGATGAAGGATTTTTACTAAAAAA‑AAGCCGCTGGGGGTGTTTTAAACCCCAGCGGCTTTTTTTTAG                                                      <  1:1912760/100‑1                                                   AAAATGAACAGTTTTGTACGTTCTGCACTATGTGTTTTAGGATTTTTACTAAAAAACGAGCCGCTGGGGGTGTTTTAAACCCCAGCGGCTTTTTTTTAGT                                                     <  1:1100305/100‑1                                                         AACAGTTTTTTATGTTCTGCACTTTGTGATTAAGGATTTTTATTAAAAAACGAGCCGCTGGGGGTGTTTTAAACCCCAGCGGCTTTTTTTTAGTAAAAAT                                               <  1:2621440/100‑1                                                           CAGTTTTGTACGTTCTGCACTATGCGATGAAGGATTTTTACTAAAAAACGAGCCGCTGGGGGTTTTTTAAACCCCAGCGGCTTTTTTTTAGTAAAAATC                                              <  2:759386/99‑1                                                                                ATGCGATGAAGGATTTTTACTAAAAAACGTGCCGCTTGGGGTGTTTTAAACCCCAGCGGCTTTTGTTTAGGAAAAATCCTTCATCGCATAGTGCAGAACG                        <  1:792687/100‑1                                                                                                    TAAAAAACGAGCCGCTGGGGGTGTTTTAAACCCCAGCGGCTTTTTTTTAGTAAAAATCCTTCATCGCATAGTGCAGAACGTACAAAACTGTTCATTTTTC    >  1:1707196/1‑100                                                                                                    TAAAAAACGAGCCGCTGGGGGTGTTTTAAACCCCAGCGGCTTTTTTTTAGTAAAAATCCTTCATAGCATAGTACAGAACGTAAAAAACTGTTCATTTTTC    >  1:2078612/1‑100                                                                                                      AAAAACGAGCCGCTGGGGGTGTTTTAAACCCCAGCGGCTTTTTTTTAGTAAAAATCCTTCATCGCATAGTGCAGAACGTACAAAACTGTTCATTTTTCAA  >  1:2667280/1‑100                                                                                                      AAAAACGAGCCGCTGGGGGTGTTTTAAACCCCAGCGGCTTTTTTTTAGTAAAAATCCTTCATCGCATAGTGCAGAACGTACAAAACTGTTCATTTTTCAA  >  2:712078/1‑100                                                                                                      AAAAACGAGCCGCTGGGGGTGTTTTAAACCCCAGCGGCTTTTTTTTAGTAAAAATCCTTCATCGCATAGTGCAGAACGTACAAAACTGTTCATTTTTCAA  <  2:807873/100‑1                                                                                                                                                                                                           TTTTTCAGGCGATTATTTGTGCGTTCGGGACGTGAATCTCTGGTGGTTGAAAAATGAACAGTTTTGTACGTTCTGCACTATGCGATGAAGGATTTTTACTAAAAAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/2405520‑2405625 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑taaaaaaCGAGCCGCTGGGGGTGTTTTAAACCCCAGCGGCTTTTTTTTAGTAAAAATCCTTCATCGCATAGTGCAGAACGTACAAAACTGTTCATTTTTCAA  <  NC_000913/2405660‑2405566

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.