New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1253895 =	38 (0.160)	49 (0.210)	13/196	23.4	0.43	intergenic (+53/+38)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
	?	NC_014034	= 3276387	91 (0.380)					intergenic (‑139/+110)	RCAP_rcc03082/RCAP_rcc03083	lipoprotein/membrane bound YbgT‑like protein
Rejected: Position hash score below cutoff.

CCCGGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCG....................................................................................................  <  NC_014034/1253996‑1253895 .....................................................................................................CGGGGGCTCCGCCCCCGGACCCCCGGCGTATTTGGGCCAAGAAGAAACGGGGGCCGGTTGCCCGGGGGGCCTTGCGCCGCATTGCCCCTTGCCCCCGTCGTG  <  NC_014034/3276387‑3276288                                                                                                                                                                                                                GGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGG                                                                                                    <  1:2804533/101‑1 (MQ=1)     GAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCTGGG                                                                                                   >  1:1477530/1‑101 (MQ=1)     GAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGG                                                                                                   <  2:644487/101‑1 (MQ=1)     GAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGG                                                                                                   <  2:334759/101‑1 (MQ=1)     GAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGG                                                                                                   <  2:292893/101‑1 (MQ=1)     GAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGG                                                                                                   >  1:3684288/1‑101 (MQ=1)     GAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCGGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGG                                                                                                   <  2:2670330/101‑1 (MQ=1)        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCT                                                                                                <  2:707858/101‑1 (MQ=1)        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCT                                                                                                >  1:2443802/1‑101 (MQ=1)         AATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTTGCCGAGGCGACCCGGGCGGGGGCT                                                                                                >  2:2800903/1‑101 (MQ=2)         AATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGggc                                                                                               >  1:672098/1‑98 (MQ=1)         AATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGggc                                                                                               >  2:1166108/1‑98 (MQ=1)          ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGgggc                                                                                              >  2:1793456/1‑97 (MQ=1)          ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCC                                                                                              <  2:2513085/101‑1 (MQ=1)          ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCC                                                                                              <  1:275521/101‑1 (MQ=1)          ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCC                                                                                              <  2:1741299/101‑1 (MQ=1)          ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCC                                                                                              <  2:3252578/101‑1 (MQ=1)            CGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGGGGGGGgggcgc                                                                                            >  2:834525/1‑95 (MQ=0)            CGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGC                                                                                            <  1:3477216/101‑1 (MQ=1)            CGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCCGGGGgggcgc                                                                                            >  1:4408131/1‑95 (MQ=0)             GCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGggccccc                                                                                           >  2:2230997/1‑94 (MQ=2)              CAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGggggcccc                                                                                          >  2:3802361/1‑93 (MQ=0)                GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCC                                                                                        <  1:2503916/101‑1 (MQ=1)                 CGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCG                                                                                       <  2:3640428/101‑1 (MQ=1)                  GCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGGCCCGCCCCCcc                                                                                      >  2:1980936/1‑99 (MQ=0)                   ccCCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCCCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGca                                                                                     <  1:821911/99‑3 (MQ=14)                   CACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCTACCC.GGCGGGGGCTCCGCCCCCGca                                                                                     <  2:3508355/101‑3 (MQ=14)                   CACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCGCCCGca                                                                                     >  1:2584647/1‑99 (MQ=1)                   CACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGca                                                                                     <  2:1892426/101‑3 (MQ=31)                   CACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCCCCCCCCCCcgc                                                                                     >  1:2294088/1‑98 (MQ=0)                    cCCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCAC                                                                                    <  1:2410000/100‑1 (MQ=17)                    ACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCAC                                                                                    <  1:1476356/101‑1 (MQ=32)                    ACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCAC                                                                                    <  1:3253765/101‑1 (MQ=32)                     CCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACC                                                                                   <  1:1325025/101‑1 (MQ=32)                     CCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACC                                                                                   <  2:289133/101‑1 (MQ=32)                       GGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCC                                                                                 <  2:3684059/101‑1 (MQ=32)                       GGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCC                                                                                 <  2:635851/101‑1 (MQ=32)                        GGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCC                                                                                <  2:2315123/101‑1 (MQ=32)                         GCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCCG                                                                               <  2:36218/101‑1 (MQ=32)                         GCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCCG                                                                               <  1:414444/101‑1 (MQ=32)                         GCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCCG                                                                               <  1:746896/101‑1 (MQ=32)                           TGCGTATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCCGag                                                                             <  1:772494/101‑3 (MQ=17)                             CGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCCGaggt                                                                           <  2:2778481/101‑5 (MQ=32)                             CGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCCGaggt                                                                           <  1:4334974/101‑5 (MQ=32)                             CGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCCGaggt                                                                           <  2:4079852/101‑5 (MQ=32)                             CGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCCGaggt                                                                           <  1:58899/101‑5 (MQ=32)                                ATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATT                                                                        <  2:4243469/101‑1 (MQ=32)                                 TCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTT                                                                       <  1:3006826/101‑1 (MQ=32)                                  CATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTa                                                                      <  2:2982337/101‑2 (MQ=32)                                                                                                                                                                                                             CCCGGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCG....................................................................................................  <  NC_014034/1253996‑1253895 .....................................................................................................CGGGGGCTCCGCCCCCGGACCCCCGGCGTATTTGGGCCAAGAAGAAACGGGGGCCGGTTGCCCGGGGGGCCTTGCGCCGCATTGCCCCTTGCCCCCGTCGTG  <  NC_014034/3276387‑3276288 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 25 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG