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.

ATTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGAAGTGAACTGCGCCACCCTGCGCGGCGATACCGCCATGTCGACGCTGTTTGGTC  >  NC_000913/3558806‑3559051                                                                                                                        |                                                                                                                               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)                                                  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)                                                                                           cGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGTGCGGCATCAGTTTAGCGGCGCGTTTGTGGAAGTGAACTGCGCCACCCTGCGCGGCGATACCGCCATGTCGACGCTg         >  3:76838/1‑149 (MQ=255)                                                                                             aTTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGAAGTGAACTGCGCCACCCTGCGCGGCGATACCGCCATGTCGACGCTGtt       <  1:143928/149‑1 (MQ=255)                                                                                                cTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGAAGTGAACTGCGCCACCCTGCGCGGCGATACCGCCATGTCGACGCTGTTTg     <  6:25463/148‑1 (MQ=255)                                                                                                 tGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGAAGTGAACTGCGCCACCCTGCTCGGCGATACCGCCATGTCGACGCTGTTTGGt   >  5:73746/1‑149 (MQ=255)                                                                                                   cTTAACGGTTCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGAAGTGAACTGCGCCACCCTGCGCGGCGATACCGCCATGTCGACGCTGTTTGGTc  <  5:110414/148‑1 (MQ=255)                                                                                                                        |                                                                                                                               ATTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTCTGCTTAACGGTCCAACCGGCGCGGGCAAGTCATTTCTGGCGCGACGCATCTTAGAGTTAAAACAGGCGCGGCATCAGTTTAGCGGCGCGTTTGTGGAAGTGAACTGCGCCACCCTGCGCGGCGATACCGCCATGTCGACGCTGTTTGGTC  >  NC_000913/3558806‑3559051

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.