New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2001919 =	NA (NA)	4 (0.050)	7/164	NT	NA	intergenic (‑130/+191)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
	?	NC_000913	2001936 =	NA (NA)					intergenic (‑147/+174)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)

ATTTATTGAATTTGCACATTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACATAAAGCGCAATTTGTCAGCAACGTGCTTCCCCGCCACCGGCGGGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2002024‑2001919 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ggcggggAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTC  >  NC_000913/2001936‑2002032                                                                                                                                                                                                             ATTTATTGAATTTGCACATTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACATAAAGCGCAATTTGTCAGCAACGTGCTTCCCCGCCACCG                                                                                                         >  1:191969/1‑100    TATTGAATTTGCACATTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACATAAAGCGCAATTTGTCAGCAACGTGCTTCCCCGCCACCGGCG                                                                                                      <  1:2236853/100‑1     ATTGAATTTGCACATTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACATAAAGCGCAATTTGTCAGCAACGTGCTTCCCCGCCACCGGCGG                                                                                                     <  1:602286/100‑1     ATTGAATTTGCACATTTTTGTAGGCCGAATAAGGCGTTTACGCCGCATCCGGCAACATAAAGCGCAACTTGTCAGCAACGCGCTTCCCCGCGACCGGCG                                                                                                      >  2:1538443/1‑99          agTTGCACATTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACATAAAGCGCAATTTGTCAGCAACGTGCTTCCCCGCCGGTGGCGGGGAAG                                                                                                <  2:357052/98‑1          ATTTGCACATTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACATAAAGCGCAATTTGTCAGCAACGTGCTTCCCCGCCGGTGGCGGGGAAG                                                                                                <  1:1997119/100‑1          ATTTGCACATTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACATAAAGCGCAATTTGTCAGCAACGTGCTTCCCCGCCGGTGGCGGGGAAG                                                                                                <  1:328094/100‑1           TTTGCACATTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACATAAAGCGCAATTTGTCAGCAACGTGCTTCCCCGCCGGTGGCGGGGAAGC                                                                                               <  1:2062375/100‑1            TTGCACATTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACATAAAGCGCAATTTGTCAGCAACGTGCTTCCCCGCCGGTGGCGGGGAAGCA                                                                                              <  1:506702/100‑1                 CATTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACATAAAGCGCAATTTGTCAGCAACGTGCTTCCCCGCCGGTGGCGGGGAAGCACGTTG                                                                                         <  1:1869802/100‑1                  ATTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACATAAAGCGCAATTTGTCAGCAACGTGCTTCCCCGCCGGTGGCGGGGAAGCACGTTGC                                                                                        <  1:1052470/100‑1                      TTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACATAAAGCGCAATTTGTCAGCAACGTGCTTCCCCGCCGGTGGCGGGGAAGCACGTTGCTGAC                                                                                    <  1:1857335/100‑1                                                                                           CCCGCCACCGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAA               >  1:1823718/1‑100                                                                                                    GGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCA      >  1:2094449/1‑100                                                                                                    GGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCA      >  1:423817/1‑100                                                                                                    GGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCA      >  1:1446492/1‑100                                                                                                      CGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAAT    >  1:996182/1‑100                                                                                                       GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATT   <  2:862183/100‑1                                                                                                        GGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTC  <  2:1875117/100‑1                                                                                                        GGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTC  >  1:1124766/1‑100                                                                                                                                                                                                             ATTTATTGAATTTGCACATTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACATAAAGCGCAATTTGTCAGCAACGTGCTTCCCCGCCACCGGCGGGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2002024‑2001919 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ggcggggAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTC  >  NC_000913/2001936‑2002032

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