New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	3558891 =	33 (0.870)	5 (0.140)	5/250	4.2	13.7%	coding (624/1599 nt)	rtcR	sigma 54‑dependent transcriptional regulator of rtcBA expression
	?	NC_000913	3558925 =	32 (0.890)					coding (658/1599 nt)	rtcR	sigma 54‑dependent transcriptional regulator of rtcBA expression
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGAAGTGAACTGCGCCACCCTGCGCGGCGATACCGCCATGT  >  NC_000913/3558751‑3559036                                                                                                                                             |                                                                                                                                                  aGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGAt                                                                                                                                           >  3:42438/1‑149 (MQ=255)             gCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACgg                                                                                                                               <  4:42438/149‑1 (MQ=255)                aTCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTcc                                                                                                                            <  5:138426/149‑1 (MQ=255)                   gCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCaa                                                                                                                          <  8:7389/148‑1 (MQ=255)                                                        aTTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCt                                                                                      >  1:117384/1‑147 (MQ=255)                                                        aTTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTa                                                                                    <  7:61150/149‑1 (MQ=255)                                                        aTTATCTTAAGTCCGGCATTGCCACGCGTAACCCGCACTTCAACCGCATGATTGATCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTa                                                                                    <  5:134370/149‑1 (MQ=255)                                                         ttttCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCTCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTag                                                                                   <  2:107333/149‑1 (MQ=255)                                                           ttCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGCGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTaga                                                                                  <  5:129791/148‑1 (MQ=255)                                                                 aGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCACCCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTaaaa                                                                           >  2:127422/1‑149 (MQ=255)                                                                         aTTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGcgcg                                                                   <  1:17034/149‑1 (MQ=255)                                                                          ttGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCgg                                                                  <  2:117384/149‑1 (MQ=255)                                                                             ccACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTaa                                                                             <  8:116164/135‑1 (MQ=255)                                                                             ccACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTaa                                                                             >  7:116164/1‑135 (MQ=255)                                                                                         cccACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTc                                                                                                     <  5:59387/99‑1 (MQ=255)                                                                                         cccACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTc                                                                                                     >  6:59387/1‑99 (MQ=255)                                                                                           cACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACTCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGgcgc                                                 <  1:127422/149‑1 (MQ=255)                                                                                               tCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGAAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCgg                                                                  <  3:110980/128‑1 (MQ=255)                                                                                                  aCCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGAGGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTtgtg                                          >  6:88833/1‑149 (MQ=255)                                                                                                  aCCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTtgtg                                          >  7:5337/1‑149 (MQ=255)                                                                                                    cGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACg                                                                                                                                >  8:44767/1‑61 (MQ=255)                                                                                                    cGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACg                                                                                                                                <  7:44767/61‑1 (MQ=255)                                                                                                         gATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGaa                                       >  5:64449/1‑145 (MQ=255)                                                                                                         gATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGaa                                       <  6:64449/145‑1 (MQ=255)                                                                                                           ttGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGAAGTGAAc                                 >  2:110080/1‑149 (MQ=255)                                                                                                                cAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGAAGTGAACTgcgc                            <  1:110080/149‑1 (MQ=255)                                                                                                                    tCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGAAGTGAACTGCGCCAcc                        <  8:5337/149‑1 (MQ=255)                                                                                                                      gAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGAAGTGAACTGCGCCACCCt                      >  7:7892/1‑149 (MQ=255)                                                                                                                        aaaaGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGAAGTGAACTGCGCCACCCTgc                    <  8:7892/149‑1 (MQ=255)                                                                                                                            gTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGAAGTGAACTGCGCCACCCTGCgcgg                >  2:143928/1‑149 (MQ=255)                                                                                                                              ggCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTTCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGAAGTGAACTGCGCCACCCTGCgcggc               >  6:110414/1‑148 (MQ=255)                                                                                                                                      aaTCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGAAGTGAACTGCGCCACCCTGCGCGGCGATACCGc       >  5:25463/1‑148 (MQ=255)                                                                                                                                          ccGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGAAGTGAACTGCGCCACCCTGCGCGGCGATACCGCCATGt  <  5:88833/149‑1 (MQ=255)                                                                                                                                             |                                                                                                                                                  AGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGAAGTGAACTGCGCCACCCTGCGCGGCGATACCGCCATGT  >  NC_000913/3558751‑3559036

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.