New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1253913 =	NA (NA)	36 (0.180)	6/164	23.3	0.34	intergenic (+71/+20)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
	?	NC_014034	= 2590221	141 (0.580)					intergenic (‑120/‑136)	glnE/RCAP_rcc02415	glutamate‑ammonia‑ligase adenylyltransferase/hypothetical protein
Rejected: Position hash score below cutoff.

TCGGCACGCAGTTCCACCCGGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCG....................................................................................................  <  NC_014034/1254012‑1253913 ....................................................................................................CGCCGAGGCGACCCGGCGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGCTAGTCTGGCG  <  NC_014034/2590221‑2590104                                                                                                                                                                                                                                               GGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGGGGG                                                                                                    >  2:2567642/1‑101 (MQ=1)                    GGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGG                                                                                                    >  2:2239745/1‑101 (MQ=1)                     GAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCCGGG                                                                                                   >  1:62400/1‑101 (MQ=1)                      AGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGGGGCGG                                                                                                  >  1:2071836/1‑101 (MQ=11)                       GAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGC                                                                                                 <  1:260268/101‑1 (MQ=1)                        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGGGCGGGgg                                                                                                >  2:1804185/1‑99 (MQ=14)                        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGTGCt                                                                                                <  2:2105458/101‑2 (MQ=1)                        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGgg                                                                                                >  2:4863526/1‑99 (MQ=1)                        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGgg                                                                                                >  1:4834091/1‑99 (MQ=1)                        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGgc                                                                                                >  1:3634218/1‑99 (MQ=1)                        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCt                                                                                                <  1:1373676/101‑2 (MQ=1)                        AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCt                                                                                                <  2:188010/101‑2 (MQ=1)                         AATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCtc                                                                                               <  1:2593273/101‑3 (MQ=1)                          ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGgggg                                                                                              >  2:1251963/1‑97 (MQ=1)                          ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCtcc                                                                                              <  1:385677/101‑4 (MQ=1)                          ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGCGGGgccc                                                                                              >  2:3701300/1‑97 (MQ=11)                           TCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCtccg                                                                                             <  2:4934030/101‑5 (MQ=1)                              CAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGggggcgcg                                                                                          >  1:3585577/1‑93 (MQ=0)                               AGCGCACCGGGCTGCGGATCAGCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCt                                                                                         <  1:50977/101‑2 (MQ=1)                                GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGgcgcgccccc                                                                                        >  1:780364/1‑91 (MQ=0)                                GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCC                                                                                        <  2:1768042/101‑1 (MQ=1)                                GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCC                                                                                        <  2:1808640/101‑1 (MQ=1)                                GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCC                                                                                        <  2:4519202/101‑1 (MQ=1)                                GCGCACCGGGCTGCGGATCATCTCGAATTTCCGGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCC                                                                                        <  1:83481/101‑1 (MQ=1)                                  GCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGGGGGGGGGCCGCCCCCCc                                                                                      >  1:3386172/1‑100 (MQ=2)                                  GCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGGTCCGCCCCCCc                                                                                      >  2:3190353/1‑100 (MQ=1)                                  GCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGAAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCgc                                                                                      <  2:2897215/101‑3 (MQ=11)                                   CACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCgca                                                                                     <  2:2696591/101‑4 (MQ=31)                                    ACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCgcac                                                                                    <  1:2638850/101‑5 (MQ=32)                                     CCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCG.CCCCCGCACC                                                                                  <  1:4507298/101‑1 (MQ=32)                                     CCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCG.CCCCCGCACC                                                                                  <  1:3069058/101‑1 (MQ=32)                                      CGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCG.CCCCCGCACCC                                                                                 <  2:312837/101‑1 (MQ=32)                                       GGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCG.CCCCCGCACCCC                                                                                <  2:2688040/101‑1 (MQ=32)                                       GGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCG.CCCCCGCACCCC                                                                                <  2:4918021/101‑1 (MQ=32)                                        GGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCG.CCCCCGCACCCCC                                                                               <  1:1693991/101‑1 (MQ=32)                                        GGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCG.CCCCCGCACCCCC                                                                               <  1:385865/101‑1 (MQ=32)                                                                                                                                                                                                                            TCGGCACGCAGTTCCACCCGGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCG....................................................................................................  <  NC_014034/1254012‑1253913 ....................................................................................................CGCCGAGGCGACCCGGCGGGGGCGCTGCCCCCCGCACCCCCCGGGATATTCGCGCCAAGATGACAGGGGCGGGGCATTTGCGCGCCTTGACCCGGGGCTTGCGGCGGCTAGTCTGGCG  <  NC_014034/2590221‑2590104 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 25 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG