New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1721522	46 (0.190)	33 (0.140)	14/196	20.6	0.29	intergenic (‑417/+29)	RCAP_rcc01588/RCAP_rcc01589	GSCFA family protein/ErfK/YbiS/YcfS/YnhG family protein
	?	NC_014034	= 2590202	113 (0.460)					intergenic (‑101/‑155)	glnE/RCAP_rcc02415	glutamate‑ammonia‑ligase adenylyltransferase/hypothetical protein
Rejected: Position hash score below cutoff.

TTCCAAATAACGCGCTGCGGGCCTCCCTCCCGCAGCGCTTTATTTTTGGCCGGTCGCCTTGGGGATTTCGCCTCGGCT.GCGCCGAGGCGACCCGCCGGG....................................................................................................  >  NC_014034/1721424‑1721522 ..................................................................................................GGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGCTAGTCTGGCGC  <  NC_014034/2590202‑2590103                                                                                                                                                                                                          TTCCAAATAACGCGCTGCGGGCCTCCCTCCCGCAGCGCTTTATTTTTGGCCGGTCGCCTTGGGGATTTCGCCTCGGCT.GCGCCGAGGCGACCCGCCGGGGG                                                                                                    >  2:4948504/1‑101 (MQ=39)    CAAATAACGCGCTGCGGGCCTCCCTCCCGCAGCGCTTTATTTTTGGCCGGTCGCCTTGGGGATTTCGCCTCGGCT.GCGCCGAGGCGACCCGCCGGGGGcgg                                                                                                 >  2:3827733/1‑98 (MQ=25)     AAATAACGCGCTGCGGGCCTCCCTCCCGCAGCGCTTTATTTTTGGCCGGTCGCCTTGGGGATTTCGCCTCGGCT.GCGCCGAGGCGACCCGCCCGGGGGggg                                                                                                >  2:2752698/1‑98 (MQ=255)     AAATAACGCGCTGCGGGCCTCCCTCCCGCAGCGCTTTATTTTTGGCCGGTCGCCTTGGGGATTTCGCCTCGGCT.GCGCCGAGGCGACCCGCCCGGCGGCGg                                                                                                >  2:3799906/1‑100 (MQ=12)     AAATAACGCGCTGCGGGCCTCCCTCCCGCAGCGCTTTATTTTCGGCCGGTCGCCTTGGGGATTTCGCCTCGGCT.GCGCCGAGGCGACCCGCCCGGGGGggg                                                                                                >  2:2570268/1‑98 (MQ=255)     AAATAACGCGATGCGGGCCTCCCTCCCGCAGCGCTTTATTTTTGGCCGGTCGCCTTGGGGATTTCGCCTCGGCT.GCGCCGAGGCGACCCGCCGGGGGGggg                                                                                                >  2:2242413/1‑98 (MQ=255)      AATAACGCGCTGCGGGCCTCCCTCCCGCAGCGCTTTATTTTTGGCCGGTCGCCTTGGGGATTTCGCCTCGGCT.GCGCCGAGGCGACCCGCCGGGGGGTGCg                                                                                               >  2:845891/1‑100 (MQ=21)      AATAACGCGCTGCGGGCCTCCCTCCCGCAGCGCTTTATTTTTGGCCGGTCGCCTTGGGGATTTCGCCTCGGCT.GCGCCGAGGCGACCCGCCCGGGGctggg                                                                                               >  2:3143570/1‑96 (MQ=255)      AATAACGCGCTGCGGGCCTCCCTCCCGCAGCGCTTTATTTTTGGCCGGTCGCCTTGGGGATTTCGCCTCGGCT.GCGCCGAGGCGACCCGCCCGGGGGGGCg                                                                                               >  2:387813/1‑100 (MQ=255)        TAACGCGCTGCGGGCCTCCCTCCCGCAGCGCTTTATTTTTGGCCGGTCGCCTTGGGGATTTCGCCTCGGCT.GCGCCGAGGCGACCCGCCGGGGGGgtcgcc                                                                                             >  2:4957594/1‑95 (MQ=12)                                                                      GCCTCGGCTGGCGCCGAGGCGACCCGGCGGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTG                                <  1:2707510/101‑1 (MQ=0)                                                                              T.GCGCCGAGGCGACCCGGCGGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGC                       <  1:2407299/101‑1 (MQ=21)                                                                                GCGCCGAGGCGACCCGGCGGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCT                      <  1:166558/101‑1 (MQ=18)                                                                                GCGCCGAGGCGACCCGGCGGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCT                      <  2:1368642/101‑1 (MQ=18)                                                                                   CCGAGGCGACCCGGCGGGGGTCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGC                   <  2:2503474/101‑1 (MQ=0)                                                                                   CCGAGGCGACCCGGCGGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGC                   <  1:1288888/101‑1 (MQ=17)                                                                                   CCGAGGCGACCCGGCGGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGC                   <  1:247255/101‑1 (MQ=17)                                                                                   CCGAGGCGACCCGGCGGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGC                   <  2:4353334/101‑1 (MQ=17)                                                                                     GAGGCGACCCGGCGGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGG                 <  1:3207939/101‑1 (MQ=17)                                                                                     GAGGCGACCCGGCGGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGG                 <  1:4828540/101‑1 (MQ=17)                                                                                       GGCGACCCGGCGGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCG               <  2:749804/101‑1 (MQ=17)                                                                                         CGACCCGGCGGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGC             <  2:3730493/101‑1 (MQ=17)                                                                                          GACCCGGCGGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGCT            <  2:2684342/101‑1 (MQ=14)                                                                                          GACCCGGCGGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGCT            <  2:1529267/101‑1 (MQ=14)                                                                                          GACCCGGCGGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGCT            <  2:4709882/101‑1 (MQ=14)                                                                                          GACCCGGCGGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGCT            <  2:1816115/101‑1 (MQ=14)                                                                                              cggCGGGTGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGCTAGTC        <  2:1979594/98‑1 (MQ=14)                                                                                              cggCGGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGCTAGTC        <  1:973285/98‑1 (MQ=14)                                                                                                 CGGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGCTAGTCTGG     <  1:2942576/101‑1 (MQ=1)                                                                                                  GGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGGTAGTCctgc    >  1:5049645/1‑97 (MQ=0)                                                                                                  GGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGGTAGGCTGGg    >  1:1845602/1‑100 (MQ=0)                                                                                                  GGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGCTAGTCTGGC    <  2:3877318/101‑1 (MQ=1)                                                                                                  GGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGCTAGTCTGGC    <  2:2508965/101‑1 (MQ=1)                                                                                                                                                                                                          TTCCAAATAACGCGCTGCGGGCCTCCCTCCCGCAGCGCTTTATTTTTGGCCGGTCGCCTTGGGGATTTCGCCTCGGCT.GCGCCGAGGCGACCCGCCGGG....................................................................................................  >  NC_014034/1721424‑1721522 ..................................................................................................GGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGCTAGTCTGGCGC  <  NC_014034/2590202‑2590103 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG