New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1253913 =	NA (NA)	22 (0.110)	7/164	29.5	0.38	intergenic (+71/+20)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
	?	NC_014034	= 2590221	72 (0.300)					intergenic (‑120/‑136)	glnE/RCAP_rcc02415	glutamate‑ammonia‑ligase adenylyltransferase/hypothetical protein
Rejected: Position hash score below cutoff.

TCGGCACGCAGTTCCACCCGGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCG...................................................................................................  <  NC_014034/1254012‑1253913 ....................................................................................................CGCCGAGGCGACCCGGCGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGCTAGTCTGGC  <  NC_014034/2590221‑2590105                                                                                                                                                                                                                                              GGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGG                                                                                                   >  1:2262720/1‑101 (MQ=1)                    GGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGG                                                                                                   >  1:3177504/1‑101 (MQ=1)                    GGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGG                                                                                                   >  1:693072/1‑101 (MQ=1)                     GAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGG                                                                                                  <  1:3548841/101‑1 (MQ=1)                      AGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGGGGGGG                                                                                                 >  1:4069719/1‑101 (MQ=1)                      AGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGG                                                                                                 <  2:4169726/101‑1 (MQ=1)                      AGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGG                                                                                                 <  2:4127384/101‑1 (MQ=1)                       GAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGC                                                                                                <  1:778416/101‑1 (MQ=1)                        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCt                                                                                               <  2:1102081/101‑2 (MQ=1)                        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCt                                                                                               <  1:523554/101‑2 (MQ=1)                         AATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCCGGGGCGC                                                                                              >  1:2919127/1‑101 (MQ=1)                          ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCtcc                                                                                             <  2:2257756/101‑4 (MQ=1)                          ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCtcc                                                                                             <  2:3873057/101‑4 (MQ=1)                             GCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCCGGGGgggcgcc                                                                                          >  2:2234407/1‑94 (MQ=0)                              CAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGgggcggcc                                                                                         >  2:183050/1‑93 (MQ=0)                               AGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCC                                                                                        <  2:3606556/101‑1 (MQ=1)                               AGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCGCCCCCCC                                                                                        >  2:4091353/1‑101 (MQ=11)                                GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCC                                                                                       <  1:1073280/101‑1 (MQ=1)                                     CCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCG.CCCCCGCACC                                                                                 <  1:4245193/101‑1 (MQ=32)                                      CGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCGGGGCCCCCCCCACC                                                                                 >  2:2731173/1‑101 (MQ=255)                                        GGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCG.CCCCCGCACCCCC                                                                              <  1:675259/101‑1 (MQ=32)                                        GGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCG.CCCCCGCACCCCC                                                                              <  2:2977579/101‑1 (MQ=32)                                                                                                                                                                                                                           TCGGCACGCAGTTCCACCCGGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCG...................................................................................................  <  NC_014034/1254012‑1253913 ....................................................................................................CGCCGAGGCGACCCGGCGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGCTAGTCTGGC  <  NC_014034/2590221‑2590105 Base quality scores:  ATCG  < 3 ≤  ATCG  < 24 ≤  ATCG  < 30 ≤  ATCG  < 34 ≤  ATCG  < 40 ≤  ATCG