New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1303942 =	109 (0.570)	4 (0.020)	4/156	24.3	0.02	intergenic (+129/+28)	urtE/RCAP_rcc01231	urea ABC transporter ATP‑binding protein UrtE/UbiH/UbiF/VisC/COQ6 family ubiquinone biosynthesis hydroxylase
	?	NC_014034	= 1478624	208 (0.850)					intergenic (+112/+31)	RCAP_rcc01372/RCAP_rcc01373	ABC transporter ATP‑binding protein/RpiR family transcriptional regulator
Rejected: Position hash score below cutoff.

CCCGA.............................................................................................................  <  NC_014034/1303946‑1303942 ............................CTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATATCCCG  <  NC_014034/1478624‑1478539      ||||||||||||||||||||||                                                                                        aagGAGGGGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGC               >  2:1275549/4‑101 (MQ=255)   gGAGGGGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTC             >  2:4979599/2‑101 (MQ=16)   gGAGGGGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTC             >  1:1688525/2‑101 (MQ=16)   gGAGGGGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTC             >  1:687427/2‑101 (MQ=16)   gGAGGGGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTC             >  1:588634/2‑101 (MQ=16)    GAGGGGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCC            <  2:458458/101‑1 (MQ=16)    GAGGGGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCC            >  2:1915627/1‑101 (MQ=19)    GAGGGGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCC            <  2:1812300/101‑1 (MQ=16)     AGGGGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCA           >  2:4859213/1‑101 (MQ=16)     AGGGGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCA           <  1:3205567/101‑1 (MQ=12)     AGGGGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCA           <  1:10402/101‑1 (MQ=12)     AGGGGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCA           <  1:2903981/101‑1 (MQ=12)      GGGGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCGCCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAA          <  2:4366554/101‑1 (MQ=255)      GGGGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAA          <  1:1211122/101‑1 (MQ=12)      GGGGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAA          <  1:2180636/101‑1 (MQ=12)       GGGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAA         <  1:3487637/101‑1 (MQ=12)       GGGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAA         <  2:4210893/101‑1 (MQ=12)       GGGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAA         >  2:3068923/1‑101 (MQ=16)        GGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAAT        <  2:4910580/101‑1 (MQ=12)        GGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAAT        <  1:488246/101‑1 (MQ=12)        GGGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAAT        <  2:4587596/101‑1 (MQ=12)         GGCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATA       >  2:2156131/1‑101 (MQ=12)          GCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATAT      <  2:1579746/101‑1 (MQ=12)          GCGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATAT      <  2:2168439/101‑1 (MQ=12)           CGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATATC     <  2:954097/101‑1 (MQ=12)           CGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATATC     <  1:4885356/101‑1 (MQ=12)           CGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATATC     >  1:4916778/1‑101 (MQ=16)           CGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATATC     <  1:1238887/101‑1 (MQ=12)           CGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATATC     <  1:5028939/101‑1 (MQ=12)           CGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATATC     <  2:1221612/101‑1 (MQ=12)           CGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATATC     <  2:2606283/101‑1 (MQ=12)           CGCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCACAGATCGTGCTTTCATCTTGCTCCAAATATC     <  1:3221035/101‑1 (MQ=255)            GCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATATCC    >  2:4289125/1‑101 (MQ=12)            GCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATATCC    >  2:4161623/1‑101 (MQ=9)            GCTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATATCC    <  2:909761/101‑1 (MQ=9)             CTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATATCCC   >  1:310201/1‑101 (MQ=12)             CTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATATCCC   <  1:4715420/101‑1 (MQ=9)             CTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATATCCC   <  2:70962/101‑1 (MQ=9)             CTGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATATCCC   <  1:2264477/101‑1 (MQ=9)              TGCCCCCCTCTTGGCCTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATATCCCG  <  1:2385195/101‑1 (MQ=9)      ||||||||||||||||||||||                                                                                        CCCGA.............................................................................................................  <  NC_014034/1303946‑1303942 ............................CTCTCGGCCAATTCACCCCCCGGGATATTTGAAGCAAGATAAATGAAAACCGCAGATCGTGCTTTCATCTTGCTCCAAATATCCCG  <  NC_014034/1478624‑1478539 Base quality scores:  ATCG  < 3 ≤  ATCG  < 23 ≤  ATCG  < 31 ≤  ATCG  < 34 ≤  ATCG  < 41 ≤  ATCG