New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 3558690	46 (1.360)	4 (0.130)	4/246	3.2	8.9%	coding (423/1599 nt)	rtcR	sigma 54‑dependent transcriptional regulator of rtcBA expression
	?	NC_000913	= 3558719	39 (1.230)					coding (452/1599 nt)	rtcR	sigma 54‑dependent transcriptional regulator of rtcBA expression
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTG  >  NC_000913/3558576‑3558859                                                                                                                                                |                                                                                                                                             aGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGt                                                                                                                                          >  4:57705/1‑148 (MQ=255)       agaagaCTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTaa                                                                                                                                   >  7:82370/1‑149 (MQ=255)        gaagaCTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAAc                                                                                                                                  >  3:39650/1‑149 (MQ=255)          agaCTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGa                                                                                                                                <  4:39650/149‑1 (MQ=255)             cTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTa                                                                                                                             <  3:47876/149‑1 (MQ=255)                tttAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTa                                                                                                                             >  1:145006/1‑146 (MQ=255)                tttAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTa                                                                                                                             <  2:145006/146‑1 (MQ=255)                        acaTCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGAt                                                                                                                  >  3:113878/1‑149 (MQ=255)                        acaTCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGACAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTaa                                                                                                                                   >  1:56685/1‑132 (MQ=255)                        acaTCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGACAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTaa                                                                                                                                   <  2:56685/132‑1 (MQ=255)                              ccaccGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGc                                                                                                            <  4:113878/149‑1 (MQ=255)                                         cACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCg                                                                                                                    >  6:147389/1‑130 (MQ=255)                                         cACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCg                                                                                                                    <  5:147389/130‑1 (MQ=255)                                         cACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGc                                                                                                 >  7:70516/1‑149 (MQ=255)                                                cgcAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTtat                                                                                                      >  4:91458/1‑137 (MQ=255)                                                cgcAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTtat                                                                                                      <  3:91458/137‑1 (MQ=255)                                                 gcAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGt                                                                                                                                          <  1:37321/100‑1 (MQ=255)                                                 gcAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGt                                                                                                                                          >  2:37321/1‑100 (MQ=255)                                                    gATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGcc                                                                                      <  3:70878/149‑1 (MQ=255)                                                     aTTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTta                                                                                                       <  8:92370/131‑1 (MQ=255)                                                     aTTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTta                                                                                                       >  7:92370/1‑131 (MQ=255)                                                                     tgGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAATAACAGCCGCGCGGCCCAGGTTAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAAc                                                                                                   <  5:152709/119‑1 (MQ=255)                                                                     tgGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAAc                                                                                                   >  6:152709/1‑119 (MQ=255)                                                                      ggCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGc                                                                     >  5:122797/1‑148 (MQ=255)                                                                             gcgcGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAAc                                                             >  8:32703/1‑149 (MQ=255)                                                                                  ttACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTg                                                        <  7:32703/149‑1 (MQ=255)                                                                                    aCCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGa                                                       <  8:82370/148‑1 (MQ=255)                                                                                    aCCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGAt                                                      >  6:64170/1‑149 (MQ=255)                                                                                     ccTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTaa                                                                                                              <  7:11364/92‑1 (MQ=255)                                                                                     ccTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTaa                                                                                                              >  8:11364/1‑92 (MQ=255)                                                                                      cTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGAttt                                                    >  3:103027/1‑149 (MQ=255)                                                                                         cccgcccgGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTc                                                  <  3:57705/148‑1 (MQ=255)                                                                                          ccgcccgGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCtt                                                <  4:103027/149‑1 (MQ=255)                                                                                            gcccgGCTGATACAATCTTCACCTCCGCTCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAACAAACGCTTGATTTTCTTaa                                              <  8:70516/149‑1 (MQ=255)                                                                                                       aCAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCtt                                                >  7:115498/1‑136 (MQ=255)                                                                                                       aCAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCtt                                                <  8:115498/136‑1 (MQ=255)                                                                                                               cACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGTCCGGCATTGCCAcgc                             <  6:122797/147‑1 (MQ=255)                                                                                                                            aaaaGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTc               >  1:144718/1‑148 (MQ=255)                                                                                                                                       cgcgcgGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGAtt   <  2:144718/149‑1 (MQ=255)                                                                                                                                        gcgcgGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACTCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGa     <  3:103002/146‑1 (MQ=255)                                                                                                                                        gcgcgGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGa     >  4:103002/1‑146 (MQ=255)                                                                                                                                        gcgcgGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTg  <  5:64170/149‑1 (MQ=255)                                                                                                                                                |                                                                                                                                             AGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGAAGTAACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTG  >  NC_000913/3558576‑3558859

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ 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.