New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_pgi	724063 =	23 (1.040)	3 (0.140)	3/268	2.9	12.6%	coding (352/2685 nt)	kdpD	fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein
	?	NC_000913_3_vch_pgi	724085 =	20 (0.950)					coding (330/2685 nt)	kdpD	fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein
Rejected: Frequency below/above cutoff threshold.

TTCCGGTGACGCCGCTGACCACATCATTCAGACTTTCCAGATGCTGAACGTTGACGGTAGTGAAAACATCAATGCCAGCTTCCAGCAGTTCTTCGATATCCTGCCAGCGTTTGGGATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGCTGATATGCCGCCCACGGTACGCCTGGCGTTTTAACGGCAGAACAGCCAGCCCTTCCAGCATGGCGGCGGTATCTTTTCG  >  NC_000913_3_vch_pgi/723937‑724222                                                                                                                                                      |                                                                                                                                          ttCCGGTGACGACGCTGACCACATCATTCAGACTTTCCAGATGCTGAACGTTGACGGTAGTGAAAACATCAATGCCAGCTTCCAGCAGTTCTTCGATATCCTGCCAGCGTTTGGGATGACGGGCACG‑TGGAGCTTCACGGTGCGCCAGt                                                                                                                                           >  1:247403/1‑149 (MQ=255)             gaagggctggctgttctgccgttaaaacgccaggcgtaccgtgggcggcatatcagcgagtttgatctcgatgccgccctcgcccgccgcccggcgctgatcttaatggacgaaCCTGGCGCATTACTGTGCGCCAGTTCGTCCATTaa                                                                                                                                >  2:300323‑M1/115‑149 (MQ=255)                      catcatTCAGACTTTCCAGATGCTGAACGTTGACGGTAGTGAAAACATCAATGCCAGCTTCCAGCAGTTCTTCGATATCCTGCCAGCGTTTGGGATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGcc                                                                                                                      >  1:260843/1‑149 (MQ=255)                          atTCAGACTTTCCAGATGCTGAACGTTGACGGTAGTGAAAACATCAATGCCAGCTTCCAGCAGTTCTTCGATATCCTGCCAGCGTTTGGGATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTa                                                                                                                                 <  2:66857/134‑1 (MQ=255)                          atTCAGACTTTCCAGATGCTGAACGTTGACGGTAGTGAAAACATCAATGCCAGCTTCCAGCAGTTCTTCGATATCCTGCCAGCGTTTGGGATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTa                                                                                                                                 >  1:66857/1‑134 (MQ=255)                             cAGACTTTCCAGATGCCGAACGTTGACGGTAGTGAAAACATCAATGCCAGCTTCCAGCAGTTCTTCGATATCCTGCCAGCGTTTGGGATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGggcggc                                                                                                               <  2:301727/149‑1 (MQ=255)                                      cAGATGCTGAACGTTGACGGTAGTGAAAACATCAATGCCAGCTTCCAGCAGTTCTTCGATATCCTGCCAGCGTTTGGGATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAggg                                                                                                      >  1:214398/1‑149 (MQ=255)                                             tGAACGTTGACGGTAGTGAAAACATCAATGCCAGCTTCCAGCAGTTCTTCGATATCCTGCCAGCGTTTGGGATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATc                                                                                               >  1:90368/1‑149 (MQ=255)                                                  gTTGACGGTAGTGAAAACATCAATGCCAGCTTCCAGCAGTTCTTCGATATCCTGCCAGCGTTTGGGATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGGGcggcgg                                                                                                             >  2:352361/1‑130 (MQ=255)                                                  gTTGACGGTAGTGAAAACATCAATGCCAGCTTCCAGCAGTTCTTCGATATCCTGCCAGCGTTTGGGATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGGGcggcgg                                                                                                             <  1:352361/130‑1 (MQ=255)                                                           aGTGAAAACATCAATGCCAGCTTCCAGCAGTTCTTCGATATCCTGCCAGCGTTTGGGATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGc                                                                                 <  1:270304/149‑1 (MQ=255)                                                                    gcgagtttgatctcgatgccgccctcgcccgccgcccggcgctgatcttaatggacgaaC‑TGGCGCATTACTGTGCGCCAGTTc                                                                                                                                         <  1:113406‑M1/25‑1 (MQ=255)                                                                    gcgagtttgatctcgatgccgccctcgcccgccgcccggcgctgatcttaatggacgaaC‑TGGCGCATTACTGTGCGCCAGTTc                                                                                                                                         >  2:113406‑M1/60‑84 (MQ=255)                                                                        aTGCCAGCTTCCAGCAGTTCTTCGATATCCTGCCAGCGTTTGGGATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGCTGATATGCCGccc                                                                    >  1:240905/1‑149 (MQ=255)                                                                                         ttcttcGATATCCTGCCAGCGTTTGGGATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGCTGATATGCCGCCCACGGTACGCCTGGCGtt                                                   <  1:333597/149‑1 (MQ=255)                                                                                            ttcGATATCCTGCCAGCGTTTGGGATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGCTGATATGCCGCCCACGGTACGCCTGGCGTTTTa                                                >  1:38014/1‑149 (MQ=255)                                                                                                atatCCTGCCAGCGTTTGGGATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGCTGATATGCCGCCCACGGTACGCCTGGCGTTTTAACgg                                            <  1:274772/149‑1 (MQ=255)                                                                                                  accccgCCAGCTGTTGGGATGCAGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTCAGAGCAGCCCCGCGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGCTGATATGCCGCCCACGGTACGCCTGGCGTTTTAACGGCa                                          <  2:303516/144‑1 (MQ=255)                                                                                                     cTGCCAGCGTTTGGGATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGggc                                                                                                                  >  1:326625/1‑74 (MQ=255)                                                                                                     cTGCCAGCGTTTGGGATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGggc                                                                                                                  <  2:326625/74‑1 (MQ=255)                                                                                                          aGCGTTTGGGATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGCTGATGTGCCGCCCACGGTACGCCTGGCGTTTTAGCGGCAGCAcagcc                                  >  1:381258/1‑149 (MQ=255)                                                                                                                   ttaatggacgaactggcgcacagtaatgcgccaggTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGCTGATATGCCGCCCACGGTACGCCTGGCGTTTTAACGGCAGAACAGCCAGCCCTTc                          >  2:300323‑M2/36‑149 (MQ=255)                                                                                                                   gATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGCTGATATGCCGCCCACGGTACGCCTGGCGTTTTAACGGCAGAACAGCCAGCCCTTcc                         <  2:214398/149‑1 (MQ=255)                                                                                                                             gaactggcgcacagtaatgcgccagTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGc                                                                                 <  1:113406‑M2/59‑1 (MQ=255)                                                                                                                             gaactggcgcacagtaatgcgccagTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGc                                                                                 >  2:113406‑M2/26‑84 (MQ=255)                                                                                                                                       ATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGCTGATATGCCGCCCACGGTACGCCTGGCGTTTTAACGGCAGAACAGCCGGCCCTTCCAGCATGGCGGCGGTATCtt      <  1:17837‑M1/149‑1 (MQ=255)                                                                                                                                       ATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGCTGATATGCCGCCCACGGTACGCCTGGCGTTTTAACGGCAGAACAGCCAGCCCTTCCAGCATGGCGGcggtaccct      <  2:9710‑M1/149‑5 (MQ=255)                                                                                                                                           cTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGCTGATATGCCGCCCACGGTACGCCTGGCGTTTTAACGGCAGAACAGCCAGCCCTTCCAGCATGGCGGCGGTATATTTTCg  >  1:231373/1‑149 (MQ=255)                                                                                                                                                      |                                                                                                                                          TTCCGGTGACGCCGCTGACCACATCATTCAGACTTTCCAGATGCTGAACGTTGACGGTAGTGAAAACATCAATGCCAGCTTCCAGCAGTTCTTCGATATCCTGCCAGCGTTTGGGATGACGGGAACC‑TGGCGCATTACTGTGCGCCAGTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGCTGATATGCCGCCCACGGTACGCCTGGCGTTTTAACGGCAGAACAGCCAGCCCTTCCAGCATGGCGGCGGTATCTTTTCG  >  NC_000913_3_vch_pgi/723937‑724222

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.