New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AM260479	= 801625	16 (0.600)	4 (0.160)	4/192	1.9	21.8%	coding (2600/5826 nt)	pilL2	Type IV pilus protein histidine kinase/response regulator hybrid PilL
	?	AM260479	= 801686	14 (0.570)					coding (2661/5826 nt)	pilL2	Type IV pilus protein histidine kinase/response regulator hybrid PilL

CCGAAGCGCGCGAGCCGGTGCCCGCGCTGCTGGCGCTGCTGCGCCGCGCCCATGCCGAGTTGTCGGCATGGGCGGCACAGCTGCATCGCGATGCGGCAACCTGGCACGACATCGCGCCGCTGGTGGCAGCCGCCGAAGCGGTGCGCGACCCGGGCGCCGCGCAGGCCGCGGATGAACTGCCAGTACTGCCCGGCGCGGCTGCGGAAGCGCCGCCCGGGCCGGCCGTCGACGCCGCCGGTCACACCGGCGCCGATG  >  AM260479/801493‑801747                                                                                                                                     |                                                                                                                           ccGAAGCGCGCGAGCCGGTGCCCGCGCTGCTGGCGCTGCTGCGCCGCGCCCATGCCGAGTTGTCGGCATGGGCGGCACAGCTGCATCGCGATGCGGCAACCTGGCACGACATCGCGCCGCTGGTGGCAgccgcc                                                                                                                           <  2:950533/134‑1 (MQ=255)     aGCGCGCGAGCCGGTGCCCGCGCTGCTGGCGCTGCTGCGCCGCGCCCATGCCGAGTTGTCGGCATGGGCGGCACAGCTGCATCGCGATGCGGCAACCTGGCACGACATCGCGCCGCTGGTGGCAGCCGCCGAAg                                                                                                                       >  1:122807/1‑134 (MQ=255)        gcgcgAGCCGGTGCCCGCGCTGCTGGCGCTGCTGCGCCGCGCCCATGCCGAGTTGTCGGCATGGGCGGCACAGCTGCATCGCGATGCGGCAACCTGGCACGACATCGCGCCGCTGGTGGCAGCCGCCGAAGCgg                                                                                                                    >  1:1006250/1‑134 (MQ=255)                                       ctgcGCCGCGCCCATGCCGAGTTGTCGGCATGGGCGGCACAGCTGCATCGCGATGCGGCAACCTGGCACGACATCGCGCCGCTGGTGGCAGCCGCCGAAGCGGTGCGCGACCCGGGCGCCGCGCAGGCCGCgg                                                                                      <  2:122807/133‑1 (MQ=255)                                       ctgcGCCGCGCCCATGCCGAGTTGTCGGCATGGGCGGCACAGCTGCATCGCGATGCGGCAACCTGGCACGACATCGCGCCGCTGGTGGCAGCCGCCGAAGCGGTGCGCGACCCGGGCGCCGCGCAGGCCGCgg                                                                                      <  2:912590/133‑1 (MQ=255)                                                   cATGCCGAGTTGTCGGCATGGGCGGCACAGCTGCATCGCGATGCGGCAACCTGGCACGACATCGCGCCGCTGGTGGCAGCCGCCGAAGCGGTgc                                                                                                                 >  2:839047/1‑94 (MQ=255)                                                   cATGCCGAGTTGTCGGCATGGGCGGCACAGCTGCATCGCGATGCGGCAACCTGGCACGACATCGCGCCGCTGGTGGCAGCCGCCGAAGCGGTgc                                                                                                                 <  1:839047/94‑1 (MQ=255)                                                                    aTGGGCGGCACAGCTGCATCGCGATGCGGCAACCTGGCACGACATCGCGCCGCTGGTGGCAgccgcc                                                                                                                           >  1:497184/1‑67 (MQ=255)                                                                    aTGGGCGGCACAGCTGCATCGCGATGCGGCAACCTGGCACGACATCGCGCCGCTGGTGGCAgccgcc                                                                                                                           <  2:497184/67‑1 (MQ=255)                                                                             acaGCTGCATCGCGATGCGGCAACCTGGCACGACATCGCGCCGCTGGTGGCAGCCGCCGAAGCGGTGCGCGACCCGGGCGCCGCGCAGGCCGCGGATGAACTGCCAGTACTGCCCGGCGCGGCTGCGGAAgcgc                                               >  2:492387/1‑134 (MQ=255)                                                                                          gATGCGGCAACCTGGCACGACATCGCGCCGCTGGTGGCAGCCGCgccgggcagtactggcagttcatccgcggcctgc                                                                                          <  2:1161129‑M1/78‑35 (MQ=255)                                                                                          gATGCGGCAACCTGGCACGACATCGCGCCGCTGGTGGCAGCCGCgccgggcagtactggcagttcatccgcggcctgc                                                                                          >  1:1161129‑M1/1‑44 (MQ=255)                                                                                          gATGCGGCAACCTGGCACGACATCGCGCCGCTGGTGGCAGCCGCCGAAGCGGTGCGCGACCCGGGCGCCgcgc                                                                                               <  1:211320/73‑1 (MQ=255)                                                                                          gATGCGGCAACCTGGCACGACATCGCGCCGCTGGTGGCAGCCGCCGAAGCGGTGCGCGACCCGGGCGCCgcgc                                                                                               >  2:211320/1‑73 (MQ=255)                                                                                          gATGCGGCAACCTGGCACGACATCGCGCCGCTGGTGGCAGCCGCCGAAGCGGTGCGCGACCCGGGCGCCGCGCAGGCCGCGGATGAACTGCCAGTACTGCCCGGCGCGGCTGCGGAAGCGCCGCCCGggccggc                                  >  1:935681/1‑134 (MQ=255)                                                                                               ggCAACCTGGCACGACATCGCGCCGCTGGTGGCAGCCGCgccgggcagtactggcagttcatccgcggcctgcgcggcgcccgg                                                                               <  1:260031‑M1/84‑46 (MQ=255)                                                                                               ggCAACCTGGCACGACATCGCGCCGCTGGTGGCAGCCGCgccgggcagtactggcagttcatccgcggcctgcgcggcgcccgg                                                                               >  2:260031‑M1/1‑39 (MQ=255)                                                                                                             aCATCGCGCCGCTGGCGGCAGCCGCCGAAGCGGTGCGCGACCCGGGCGCCGCGCAGGCCGCGGATGAACTGCCAGTACTGCCCGGCGCGGCTGCGGa                                                    >  2:1160119/1‑97 (MQ=255)                                                                                                             aCATCGCGCCGCTGGCGGCAGCCGCCGAAGCGGTGCGCGACCCGGGCGCCGCGCAGGCCGCGGATGAACTGCCAGTACTGCCCGGCGCGGCTGCGGa                                                    <  1:1160119/97‑1 (MQ=255)                                                                                                                           gtggCAGCCGCCGAAGCGGTGCGCGACCCGGGCGCCGCGCAGGCCGCGGATGAACTGCCAGTACTGCCCGGCGCGGCTGCGGAAGCGCCGCCCGGGCCGGCCGTCGACGCCGCCGGTCACACCGGCGCCGATg  <  1:514015/133‑1 (MQ=255)                                                                                                                                     |                                                                                                                           CCGAAGCGCGCGAGCCGGTGCCCGCGCTGCTGGCGCTGCTGCGCCGCGCCCATGCCGAGTTGTCGGCATGGGCGGCACAGCTGCATCGCGATGCGGCAACCTGGCACGACATCGCGCCGCTGGTGGCAGCCGCCGAAGCGGTGCGCGACCCGGGCGCCGCGCAGGCCGCGGATGAACTGCCAGTACTGCCCGGCGCGGCTGCGGAAGCGCCGCCCGGGCCGGCCGTCGACGCCGCCGGTCACACCGGCGCCGATG  >  AM260479/801493‑801747

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ 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.