New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	2707710 =	42 (0.930)	4 (0.090)	4/282	6.1	8.2%	noncoding (69/98 nt)	RIP188 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP188 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
	?	CP009273	2939352 =	50 (1.170)					intergenic (‑151/+88)	tcdA/mltA	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA/membrane‑bound lytic murein transglycosylase A
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CCGCAAACGACAGAAGAGTAATCTCAATGCCAGGTTTAAGCCTGGTATTAAAAGTGCTGGCAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTATTTTTATCCAGCCACAAAACTCTCTTCAACACACTGAATAAAAGTGTGCATCGCCGGGCTAAC  >  CP009273/2707569‑2707857                                                                                                                                              |                                                                                                                                                     ccGCAAACGACAGAAGAGTAAGCTCAATGCCAGGTTTAAGCCTGGTATTAAAAGTGCTGGCAAACGCAAACCTGCCTGATGCGCTACGCTTATCAGGCCTACGTGCCCCCTGAAATATATTGAATTTGCCCGAGCTTGTAGGCCGGAtc                                                                                                                                               >  2:68643/1‑148 (MQ=25)   gCAAACGACAGAAGAGTAATCTCAATGCCAGGTTTAAGCCTGGTATTAAAAGTGCTGGCAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAg                                                                                                                                             <  1:123045/149‑1 (MQ=255)                   tAATCTCAATGCCAGGTTTAAGCCTGGTATTAAAAGTGCTGGCAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTCCGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGGGTTCCCGCCGCATc                                                                                                                             >  1:562331/1‑149 (MQ=255)                        tcAATGCCAGGTTTAAGCCTGGTATTAAAAGTGCTGGCAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCa                                                                                                                        >  2:534182/1‑149 (MQ=255)                              ccAGGTTTAAGCCTGGTATTAAAAGTGCTGGCAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATa                                                                                                                  >  1:611036/1‑149 (MQ=255)                                    ttAAGCCTGGTATTAAAAGTGCTGGCAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAgcgc                                                                                                            >  1:39032/1‑149 (MQ=255)                                    ttAAGCCTGGTATTAAAAGTGCTGGCAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCACCCGGCATGAATAAAccgc                                                                                                            >  2:282259/1‑149 (MQ=255)                                         ccTGGTATTAAAAGTGCTGGCAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACttt                                                                                                       >  1:100444/1‑149 (MQ=255)                                         ccTGGTATTAAAAGTGCTGGCAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACCCCGCATCCGGCATGCATAAAgcggcgctt                                                                                                       >  1:446409/1‑143 (MQ=255)                                          cTGGTATTAAAAGTGCTGGAAAATGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTg                                                                                                      >  2:500270/1‑149 (MQ=255)                                           tGGTATTAACAGTTCTGGCACAGGCAAAACTGCCTGATGGGTTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGt                                                                                                     <  1:463778/149‑1 (MQ=18)                                            ggTATTAAAAGTGCTGGCAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGATTTAAGCGCACTTTGTc                                                                                                    >  1:462668/1‑149 (MQ=255)                                                  aaaaGTGCTGGCAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAg                                                                                              >  2:460353/1‑149 (MQ=255)                                                      gTGCTGGCAAACGCAAAAATGCCTGATGCGCTACGCTTCTCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCGCGATCTTTTAGGGGGAATAAGGCGTTCACGCCGCGTCAGGCATGAATACAGAGCACTTTGTGGACAGCTTaa                                                                                          >  2:299939/1‑149 (MQ=18)                                                          tGGCAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGc                                                                                      <  2:521370/149‑1 (MQ=255)                                                              aaaCGCAAACCTGCCTGAGGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCggg                                                                                  <  2:297493/149‑1 (MQ=255)                                                              aaaCGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCggg                                                                                  >  1:665022/1‑149 (MQ=255)                                                                  gCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTCTa                                                                              >  1:198338/1‑149 (MQ=255)                                                                    aaaaCTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATGCGGCCTGAATAAAGCGCACTTTGTCGACAAGTTGAATGCGGGGTTTAAt                                                                            >  2:337512/1‑149 (MQ=255)                                                                    aaaaCTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAAt                                                                            >  1:365531/1‑149 (MQ=255)                                                                    aaaaCTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAAt                                                                            >  1:735620/1‑149 (MQ=255)                                                                              gaggggcTACGCTTATCAGCCCTACGTGGCTCATGCCATACATTTAATTTGCACGACCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACatta                                                                 <  2:9760/144‑1 (MQ=25)                                                                                 gcgcTACGCTTATGAGGCCTACGTGGATCATCCAATATATGTAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTAttt                                                              <  1:647475/149‑1 (MQ=25)                                                                                  cgcTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTAtttt                                                             >  1:513399/1‑149 (MQ=255)                                                                                   gttACGCTTATCAGGCCTACTTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTAttttt                                                            <  2:53241/147‑1 (MQ=255)                                                                                            aTCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCAAGATCTTGTCGGCCGGATAAGGCGTTCAGGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTATTTTTATCCAGCca                                                   >  1:293890/1‑149 (MQ=255)                                                                                             tCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTATTTTTATCCAGCcac                                                  >  1:5547/1‑149 (MQ=255)                                                                                                        tggaccATGCAATATATTGAAATCGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCAGCG‑TTATTCGTGGTCATTATTTTTATCCAGCCACAAAACTCTCtt                                       <  1:359202/144‑1 (MQ=21)                                                                                                        tGGCTCTTGCACTAGATTGAATTTGCACGGTCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATTAAGCTCACTTTGTCGACTAGTTAAATGCCGGGTTTAATC‑CCGACATTATTTTTATCCAGCCACAAAACTCTCtt                                       <  1:588565/149‑1 (MQ=37)                                                                                                           cTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTATTTTTATCCAGCCACAGAACTCTCTTCaa                                    >  2:275836/1‑149 (MQ=255)                                                                                                            tCATGTAATATACTGAATTTGTCCGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTATTTTTATCCAGCCACAAAACTCTCTTCAac                                   <  1:392488/149‑1 (MQ=255)                                                                                                            tCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTATTTTTATCCAGCCACAAAACTCTCTTCAac                                   >  1:731732/1‑149 (MQ=255)                                                                                                              aTGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTATTTTTATCCAGCCACAAAACTCTCTTCAacac                                 >  1:692326/1‑149 (MQ=255)                                                                                                               tGCAATATTTTGAAGGTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTATTTTTATCCAGCCACAAAACTCTCTTCAacaca                                <  1:565764/149‑1 (MQ=255)                                                                                                                ccAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCTTCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTATTTTTATCCAGCCACAAAACTCTCTTCAacacac                               <  1:689508/148‑1 (MQ=255)                                                                                                                             gttGCACGATCTTGTAGGCCGGATAAGGCGCTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTATTTTTATCCAGCCACAAAACTCTCTTCAACACACTGAATAAAAgtgt                  >  2:696288/2‑149 (MQ=255)                                                                                                                                 cACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTATTTTTATCCAGCCACAAAACTCTCTTCAACACCCCGAATAAAAGTGTGCAt              >  1:245691/1‑149 (MQ=255)                                                                                                                                 cACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTATTTTTATCCAGCCACAAAACTCTCTTCAACACACTGAATAAAAGTGTGCAt              >  2:600190/1‑149 (MQ=255)                                                                                                                                 cACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTATTTTTATCCAGCCACAAAACTCTCTTCAACACACTGAATAAAAGTGTGCAt              >  2:682384/1‑149 (MQ=255)                                                                                                                                       ctgggaGGCCGGACAAGGCGTTCACGCCGCATCCCGCATGAATAAAGCGCACTTTGTCGACAAGTAAAATGCCGGGTTTAATC‑CCTACATTATTTTTATCCAGCCACAAAACTCGCTTCAACACACTGAATAAAAGTGTGCATCGCCgg        <  2:623486/144‑1 (MQ=38)                                                                                                                                       cTTGGAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGCCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTATTTTTATCCAGCCACAAAACTCTCTTCAACACACTGAATAAAAGTGTGCATCGCCgg        <  1:243725/149‑1 (MQ=255)                                                                                                                                           catgCCGGATGCGGCGTGAACGCCTTATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTATTTTTATCCAGCCACAAAACTCTCTTCAACACACTGAATAAAAGTGTGCATCGCCGGGCTa    >  1:373042/4‑149 (MQ=38)                                                                                                                                             ggCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTATTTTTATCCAGCCACAAAACTCTCTTCAACACACTGAATAAAAGTGTGCATCGCCGGGCTAAc  <  1:700293/149‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                     CCGCAAACGACAGAAGAGTAATCTCAATGCCAGGTTTAAGCCTGGTATTAAAAGTGCTGGCAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGCTCATGCAATATATTGAATTTGCACGATCTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTTTGTCGACAAGTTAAATGCCGGGTTTAATC‑CCGACATTATTTTTATCCAGCCACAAAACTCTCTTCAACACACTGAATAAAAGTGTGCATCGCCGGGCTAAC  >  CP009273/2707569‑2707857

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.