New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	4969573 =	26 (1.510)	4 (0.260)	4/252	1.5	14.1%	coding (715/2064 nt)	fliC	flagellin
	?	NC_002947	= 4969569	25 (1.610)					coding (719/2064 nt)	fliC	flagellin
Rejected: Frequency below/above cutoff threshold.

CGATGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCATTGTTGGTGCCGAACT  >  NC_002947/4969432‑4969704                                                                                                                                          |                                                                                                                                        cGATGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtgg                                                                                                                             >  1:332633‑M2/1‑138 (MQ=255)              cTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGtt                                                                                                                <  2:305413/150‑1 (MQ=255)                              ttCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCg                                                                                                >  2:8511/1‑150 (MQ=255)                                                cTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtggtaccaacgttcagcaccaagttaccggcagcagcaccgatggtcggc                                                                              <  1:312662‑M2/150‑60 (MQ=255)                                                    cAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGAAGCCCCGATAGTCgcat                                                                          >  2:128932/1‑147 (MQ=255)                                                     aaTGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCtt                                                                         >  1:158022/1‑150 (MQ=255)                                                             cGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATa                                                                 <  1:352676/150‑1 (MQ=255)                                                                     ccGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtggtaccaacgttcagcaccaagttaccggcagcagcaccgatggtcggcttatcaaatacgcccgcgcct                                                         >  2:312662‑M2/1‑70 (MQ=255)                                                                      cGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCgcgc                                                        >  2:375823/1‑150 (MQ=255)                                                                         tATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACGGATGGTCGGCTTATCAAATACGCCCGCGCCTg                                                     >  2:354227/1‑150 (MQ=255)                                                                                      cAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCa                                                   >  1:311010/1‑139 (MQ=255)                                                                                      cAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCa                                                   <  2:311010/139‑1 (MQ=255)                                                                                         gTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtggtg                                                                                                                           <  1:211846/64‑1 (MQ=255)                                                                                         gTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtggtg                                                                                                                           >  2:211846/1‑64 (MQ=255)                                                                                           tGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAg                                   <  2:158022/150‑1 (MQ=255)                                                                                            gATATTGTCAACCACATCCTGCAGGGTGTCGGCTGCCGCAGCAGCGAtggtggtggttgttttccttgatcgtatcaccaagttaccggcagcagcaccgatggtcggcttatcaaatacgcccgcgcctgcagtacccacaaccgaagc                                  >  1:316719‑M2/1‑47 (MQ=255)                                                                                             atatCGTCAACCACATCCTGCAGGGTATCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCa                                 >  2:215620/1‑150 (MQ=255)                                                                                                         acaTCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCCAACAAGGCCGCGCCTGCAGTACCCACCACCGAAGCAGAAGTGCTGCCa                     >  1:89746/1‑150 (MQ=255)                                                                                                           aTCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtggtaccaacgttcagcaccaagttaccggcagcagcaccgatggtcggcttatcaaatacgcccgcgcctgcagtacccacaaccgaagcagaagtgctgccagcatt                   <  2:338595‑M2/150‑119 (MQ=255)                                                                                                               tGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCCCCGGCGGTGGTCGGAACATAAAATAGGCACCCAGGCCTAGGAGCCATGACCGAAGCAGAAGTGCTGCCAGCAtcg               >  1:398728/1‑148 (MQ=255)                                                                                                               tGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACAGAAGCAGAAGTGCTGCCAGCAttg               >  1:362861/1‑150 (MQ=255)                                                                                                                      tgtCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCa                                                   >  1:348435/1‑107 (MQ=255)                                                                                                                      tgtCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCa                                                   <  2:348435/107‑1 (MQ=255)                                                                                                                      tgtCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACAGAAGCAGAAGTGCTGCCAGCATTGTTGGTGc        <  2:362861/150‑1 (MQ=255)                                                                                                                        tCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGaa                              <  2:164141/126‑1 (MQ=255)                                                                                                                        tCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGaa                              >  1:164141/1‑126 (MQ=255)                                                                                                                          gCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCATTGTTGGTGCCGaa    >  2:345606/1‑150 (MQ=255)                                                                                                                            cTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCATTGTTGGTGCCTAACt  <  1:8511/150‑1 (MQ=255)                                                                                                                               ccGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGtgctgc                       <  2:272692/126‑1 (MQ=255)                                                                                                                               ccGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGtgctgc                       >  1:272692/1‑126 (MQ=255)                                                                                                                                          |                                                                                                                                        CGATGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCATTGTTGGTGCCGAACT  >  NC_002947/4969432‑4969704

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ 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.