New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	3559450 =	10 (0.800)	4 (0.330)	4/248	1.1	34.0%	coding (1183/1599 nt)	rtcR	sigma 54‑dependent transcriptional regulator of rtcBA expression
	?	NC_000913_3_pae_tpiA	3559496 =	6 (0.500)					coding (1229/1599 nt)	rtcR	sigma 54‑dependent transcriptional regulator of rtcBA expression

CGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGCGCCAGGAAGATATTGAACCGAACCTGGATTATGAAGTGGAGCGCCACGCCTCACTCACTGGCGACAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAA  >  NC_000913_3_pae_tpiA/3559311‑3559578                                                                                                                                            |                                                                                                                                 cgcgcgGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGCGCCAGGAAGATATTGAACCGAACCTGGATTATGAAGTGGAGCGCCACGCCTCACTCACTGGCGACAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGtt                                                                                                                        >  3:35076/1‑150 (MQ=255)    gcgGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGCGCCAGGAAGATATTGAACCGAACCTGGATTATGAAGTGGAGCGCCACGCCTCACTCACTGGCGACAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGc                                                                                                                     >  4:30300/1‑150 (MQ=255)      ggATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGCGCCAGGAAGATATTGAACCGAACCTGGATTATGAAGTGGAGCGCCACGCCTCACTCACTGGCGACAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCtt                                                                                                                   <  1:76395/150‑1 (MQ=255)                          aCCCTGCCGGGTCTACGCCAGCGCCAGGAAGATATTGAACCGAACCTGGATTATGAAGTGGAGCGCCACGCCTCACTCACTGGCGACAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCa                                                                                               <  3:50381/150‑1 (MQ=255)                                               cgccagGAAGATATTGAACCGAACCTGGATTATGAAGTGGAGCGCCACGCCTCACTCACTGGCGACAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTcgc                                                                          <  4:58194/150‑1 (MQ=255)                                                  cagGAAGATATTGAACCGAACCTGGATTATGAAGTGGAGCGCCACGCCTCACTCACTGGCGACAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGaa                                                                       <  2:120278/150‑1 (MQ=255)                                                                acgtccagagtgatgcgtccgctagtggcaaaggtggccatccgcgtgacgctggcagaaagttcgcgaaagttacCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGt                                                                                   <  1:42355‑M1/48‑1 (MQ=255)                                                                acgtccagagtgatgcgtccgctagtggcaaaggtggccatccgcgtgacgctggcagaaagttcgcgaaagttacCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGt                                                                                   >  2:42355‑M1/77‑124 (MQ=255)                                                                                 tccgctagtggcaaaggtggccatccgcgtgacgctggcagaaagttcgcgaaagttacCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTa                                                                                  <  3:34409‑M1/49‑1 (MQ=255)                                                                                 tccgctagtggcaaaggtggccatccgcgtgacgctggcagaaagttcgcgaaagttacCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTa                                                                                  >  4:34409‑M1/60‑108 (MQ=255)                                                                                                                 aGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTg        <  1:39566/150‑1 (MQ=255)                                                                                                                       cgtTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGaa  <  3:30300/150‑1 (MQ=255)                                                                                                                              acacCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGc                                    <  1:131398/109‑1 (MQ=255)                                                                                                                              acacCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGc                                    >  2:131398/1‑109 (MQ=255)                                                                                                                                            |                                                                                                                                 CGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGCGCCAGGAAGATATTGAACCGAACCTGGATTATGAAGTGGAGCGCCACGCCTCACTCACTGGCGACAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAA  >  NC_000913_3_pae_tpiA/3559311‑3559578

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