New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 4957743	56 (1.240)	9 (0.210)	9/234	NT	14.5%	coding (1002/1020 nt)	fliG	flagellar motor switch protein
	?	NC_002947	= 4957750	53 (1.240)					coding (995/1020 nt)	fliG	flagellar motor switch protein

GAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/4957609‑4957743 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ctcggcgGCAAGGGCGCCGAGGAAATGATCTAAGGTATTCGCGATCCCATAGCCGACGCCGCCTTTTGTAGGAGCGGGTTTACCCGCGAAGGCGTCGGTCCTGGCAATCGAGGTTGTCGCTGCCGACGCATTCGCGGGTGAACCCGCTCCTACAAG  <  NC_002947/4957750‑4957602                                                                                                                                                                                                                                                                                              GAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGGCAAGGGCGCCGAGG                                                                                                                                        <  2:675983/150‑1                       GTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCG                                                                                                                                                          <  1:490263/110‑1                       GTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCG                                                                                                                                                          >  2:490263/1‑110                                                                     AAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTGCTCGGCGGCAAGGGCGCCGAGGAAA                                                                                                                                     <  1:900640/85‑1                                                                     AAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTGCTCGGCGGCAAGGGCGCCGAGGAAA                                                                                                                                     >  2:900640/1‑85                                                                         CCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCC                                                                                                                                                             >  1:859622/1‑57                                                                         CCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCC                                                                                                                                                             <  2:859622/57‑1                                                                                TACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGGCAAGGGCGCCGA                                                                                                                                          <  1:1064837/69‑1                                                                                TACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCGGCAAGGGCGCCGA                                                                                                                                          >  2:1064837/1‑69                                                                                                                    CTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGGAAATGATCTAAGGTATTCGCGATCCCATAGCCGACGCCGCCTTTTGTAGGAGCGG                                                                                 <  1:840386/90‑1                                                                                                                    CTTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGGAAATGATCTAAGGTATTCGCGATCCCATAGCCGACGCCGCCTTTTGTAGGAGCGG                                                                                 >  2:840386/1‑90                                                                                                                     TTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGGAAATGATCTAAGGTATTCGCGATCCCATAGCCGACGCCGCCTTTTGTAGGAGCGGGTTTACCCGCGAAGGCGTCGGTCCTGGCAATCGAGGT                                            <  1:15494/126‑1                                                                                                                     TTAGATCATTTCCTCGGCGCCCTTGCCGCCGAGGAAATGATCTAAGGTATTCGCGATCCCATAGCCGACGCCGCCTTTTGTAGGAGCGGGTTTACCCGCGAAGGCGTCGGTCCTGGCAATCGAGGT                                            >  2:15494/1‑126                                                                                                                                  TCGGCGGCAAGGGCGCCGAGGAAATGATCTAAGGTATTCGCGATCCCATAGCCGACGCCGCCTTTTGTAGGAGCGGGTTTACCCGCGAAGGCGTCGGTCCTGGCAATCGAGGTTGTCGCTGCCGACGCATTCGCGGGTGAACCCGCTCCT       >  2:825329/1‑150                                                                                                                                    GGCGGCAAGGGCGCCGAGGAAATGATCTAAGGTATTCGCGATCCCATAGCCGACGCCGCCTTTTGTAGGAGCGGGTTTACCCGCGAAGGCGTCGGTCCTGGCAATCGAGGTTGTCGCTGCCGACGCATTCGCGGGTGAACCCGCTCCTAC     >  1:358968/1‑150                                                                                                                                       GGCAAGGGCGCCGAGGAAATGATCTAAGGTATTCGCGATCCCATAGCCGACGCCGCCTTTTGTAGGAGCGGGTTTACCCGCGAAGGCGTCGGTCCTGGCAATCGAGGTTGTCGCTGCCGACGCATTCGCGGGTGAACCCGCTCCTACAAG  >  2:18481/1‑150                                                                                                                                                                                                                                                                                              GAGCGGGTTCACCCGCGAATGCGTCGGCAGCGACAACCTCGATTGCCAGGACCGACGCCTTCGCGGGTAAACCCGCTCCTACAAAAGGCGGCGTCGGCTATGGGATCGCGAATACCTTAGATCATTTCCTCGGCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/4957609‑4957743 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ctcggcgGCAAGGGCGCCGAGGAAATGATCTAAGGTATTCGCGATCCCATAGCCGACGCCGCCTTTTGTAGGAGCGGGTTTACCCGCGAAGGCGTCGGTCCTGGCAATCGAGGTTGTCGCTGCCGACGCATTCGCGGGTGAACCCGCTCCTACAAG  <  NC_002947/4957750‑4957602

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ 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.