New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1253895 =	93 (0.250)	67 (0.180)	14/164	28.8	0.28	intergenic (+53/+38)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
	?	NC_014034	= 2590203	257 (0.560)					intergenic (‑102/‑154)	glnE/RCAP_rcc02415	glutamate‑ammonia‑ligase adenylyltransferase/hypothetical protein
Rejected: Position hash score below cutoff.

TCGGCACGCAGTTCCACCCGGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCG....................................................................................................  <  NC_014034/1254012‑1253895 ....................................................................................................CGCCGAGGCGACCC.GGCGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGCTAGTCTGGCG  <  NC_014034/2590203‑2590104                                                                                                                                                                                                                                               CGGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGG                                                                                                     >  1:6296051/1‑101 (MQ=1)                   CGGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGG                                                                                                     >  2:3856785/1‑101 (MQ=1)                    GGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGG                                                                                                    >  1:142184/1‑101 (MQ=1)                    GGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGG                                                                                                    <  2:5707086/101‑1 (MQ=1)                    GGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCCGG                                                                                                    >  1:5053519/1‑101 (MQ=1)                    GGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCCGG                                                                                                    >  1:7643114/1‑101 (MQ=1)                     GAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGCGGCGACCC.GGCGGGG                                                                                                   >  2:8341546/1‑101 (MQ=1)                      AGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGG                                                                                                  >  2:6121955/1‑101 (MQ=1)                       GAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGGCGGGGG                                                                                                  >  1:1877496/1‑101 (MQ=11)                       GAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCCGGGGg                                                                                                 >  2:280372/1‑100 (MQ=1)                        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGcatg                                                                                                <  2:4331217/101‑5 (MQ=1)                        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGgg                                                                                                >  2:475652/1‑99 (MQ=1)                        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGgg                                                                                                >  1:2702243/1‑99 (MQ=1)                        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGgc                                                                                                >  2:6545792/1‑99 (MQ=1)                        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCt                                                                                                >  2:4816373/1‑100 (MQ=1)                        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCt                                                                                                <  2:7017969/101‑2 (MQ=1)                        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCt                                                                                                <  2:7903739/101‑2 (MQ=1)                        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCc                                                                                                >  2:4986313/1‑100 (MQ=1)                         AATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCTGGGGCGC                                                                                               >  2:1235628/1‑101 (MQ=1)                         AATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGggg                                                                                               >  2:6031137/1‑98 (MQ=1)                         AATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGgcc                                                                                               >  1:8770299/1‑98 (MQ=1)                          ATCGCAGTGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCtcc                                                                                              <  1:7077297/101‑4 (MQ=1)                          ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGgtcc                                                                                              >  2:3454441/1‑97 (MQ=1)                          ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGgggc                                                                                              >  2:137421/1‑97 (MQ=1)                          ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGGGCc                                                                                              >  1:9083315/1‑100 (MQ=1)                          ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCtcc                                                                                              <  2:8340626/101‑4 (MQ=1)                          ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCtcc                                                                                              <  1:6252050/101‑4 (MQ=1)                          ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCtcc                                                                                              <  2:555277/101‑4 (MQ=1)                          ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCtcc                                                                                              <  2:4784073/101‑4 (MQ=1)                          ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCtcc                                                                                              <  1:2593928/101‑4 (MQ=1)                            CGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCCGGGGGGCgcg                                                                                            >  2:3327251/1‑98 (MQ=0)                             GCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGgtccgcc                                                                                           >  2:8736253/1‑94 (MQ=1)                             GCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCC                                                                                           <  2:1070970/101‑1 (MQ=1)                             GCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCC                                                                                           <  2:5675098/101‑1 (MQ=1)                              CAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGgtcccccc                                                                                          >  1:5956682/1‑93 (MQ=0)                              CAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCC                                                                                          <  1:2103702/101‑1 (MQ=1)                               AGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGGGGGGGGGCCGCCCC                                                                                         >  2:7607535/1‑101 (MQ=0)                               AGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCC                                                                                         >  2:7626893/1‑101 (MQ=1)                               AGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCC                                                                                         <  2:5197046/101‑1 (MQ=1)                                GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGTCCC.GGCGGGGGCTCCGCCCCC                                                                                        <  1:9189978/101‑1 (MQ=1)                                GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCC                                                                                        <  2:8165954/101‑1 (MQ=1)                                GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCC                                                                                        <  1:6122192/101‑1 (MQ=1)                                GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCC                                                                                        <  2:3660782/101‑1 (MQ=1)                                GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCC                                                                                        <  1:8249661/101‑1 (MQ=1)                                GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCC                                                                                        <  2:5925086/101‑1 (MQ=1)                                GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCC                                                                                        <  1:2750882/101‑1 (MQ=1)                                 CGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCtcccgccccc                                                                                       >  2:8283417/1‑91 (MQ=0)                                 CGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCg                                                                                       <  1:8556298/101‑2 (MQ=1)                                 CGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCg                                                                                       <  1:3149522/101‑2 (MQ=1)                                 CGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCg                                                                                       <  2:2499002/101‑2 (MQ=1)                                  GCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGGTCCGCCCCCgc                                                                                      >  2:3658425/1‑99 (MQ=11)                                  GCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGGGCCGCCCCCCc                                                                                      >  2:1815223/1‑100 (MQ=2)                                  GCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCgc                                                                                      <  1:6582211/101‑3 (MQ=11)                                   CACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGGGCCGCCCCCCcc                                                                                     >  1:1088963/1‑99 (MQ=2)                                   CACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGGGCCCCCCCCCcc                                                                                     >  1:7277513/1‑99 (MQ=2)                                    cCCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCgcac                                                                                    <  2:400752/100‑5 (MQ=17)                                    ACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCgcac                                                                                    <  1:3938966/101‑5 (MQ=32)                                     CCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCG.CCCCCGCACC                                                                                  <  1:779195/101‑1 (MQ=32)                                      CGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGGGCCGCCCCCCccccc                                                                                  >  1:6211560/1‑96 (MQ=255)                                      CGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCCccccc                                                                                  >  2:8754487/1‑96 (MQ=0)                                      CGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCG.CCCCCGCACCC                                                                                 <  1:5883511/101‑1 (MQ=32)                                       GGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCG.CCCCCGCACCCC                                                                                <  2:3206749/101‑1 (MQ=32)                                       GGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCG.CCCCCGCACCCC                                                                                <  2:3092275/101‑1 (MQ=32)                                       GGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCG.CCCCCGCACCCC                                                                                <  1:8592566/101‑1 (MQ=32)                                        GGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCG.CCCCCGCACCCCC                                                                               <  2:1461199/101‑1 (MQ=32)                                        GGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCG.CCCCCGCACCCCC                                                                               <  1:8775277/101‑1 (MQ=32)                                        GGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCG.CCCCCGCACCCCC                                                                               <  1:6102354/101‑1 (MQ=32)                                                                                                                                                                                                                             TCGGCACGCAGTTCCACCCGGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCG....................................................................................................  <  NC_014034/1254012‑1253895 ....................................................................................................CGCCGAGGCGACCC.GGCGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGCTAGTCTGGCG  <  NC_014034/2590203‑2590104 Base quality scores:  ATCG  < 3 ≤  ATCG  < 23 ≤  ATCG  < 31 ≤  ATCG  < 34 ≤  ATCG  < 41 ≤  ATCG