New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	974316 =	2 (0.010)	44 (0.200)	11/182	28.3	0.75	intergenic (+196/+63)	RCAP_rcc00884/RCAP_rcc00885	hypothetical protein/hypothetical protein
	?	NC_014034	= 1253890	27 (0.110)					intergenic (+48/+43)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
Rejected: Position hash score below cutoff.

GGGGTATTTCGCCTCGGCTGTCGCCGAGGCGACCCGCCGGGGGCT...........................................................................................................  <  NC_014034/974360‑974316 ....................................................CGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCACC  <  NC_014034/1253890‑1253791                                              |||||||                                                                                                     agaggATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTT                                                     <  2:2745360/96‑1 (MQ=32)   aggATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTA                                                   <  1:4383723/98‑1 (MQ=32)   aggATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTA                                                   <  1:4270036/98‑1 (MQ=32)   aggATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTA                                                   <  1:3380305/98‑1 (MQ=32)    ggATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTAT                                                  <  2:3645734/99‑1 (MQ=32)      ATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTT                                                <  1:3902527/101‑1 (MQ=32)       TTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTC                                               <  2:3503396/101‑1 (MQ=32)       TTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTC                                               <  2:2113155/101‑1 (MQ=32)       TTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTC                                               <  1:2234569/101‑1 (MQ=32)          CGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCC                                            <  1:783322/101‑1 (MQ=32)            CCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTC                                          <  2:1689067/101‑1 (MQ=32)             CTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCG                                         <  2:982152/101‑1 (MQ=32)               ctGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAA                                       <  2:127260/99‑1 (MQ=17)               CGGCTTGCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAA                                       <  1:738222/101‑1 (MQ=17)                 GCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGG                                     <  1:1721005/101‑1 (MQ=32)                 GCTTTCGCCGAGGCCACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGG                                     <  2:2060095/101‑1 (MQ=17)                  cttgCGCCGAGGCGCCCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGC                                    <  2:1006875/97‑1 (MQ=9)                  cttTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGC                                    <  2:2262558/98‑1 (MQ=32)                   ttTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCG                                   <  2:4232208/99‑1 (MQ=32)                    tTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGC                                  <  1:4611520/100‑1 (MQ=32)                     TCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCA                                 <  2:1197148/101‑1 (MQ=32)                       GCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGC                               <  1:2660146/101‑1 (MQ=32)                         CGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCATCCG                             <  2:1648559/101‑1 (MQ=17)                          GAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGCGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGG                            <  2:2384015/101‑1 (MQ=17)                            GGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTC                          <  2:2007560/101‑1 (MQ=32)                              CGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTG                        <  2:3707548/101‑1 (MQ=32)                               GACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGG                       <  1:4238626/101‑1 (MQ=32)                               GACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGG                       <  1:2649444/101‑1 (MQ=32)                                 CCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAA                     <  1:294397/101‑1 (MQ=32)                                 CCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAA                     <  1:3695250/101‑1 (MQ=32)                                    ggCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCC                  <  1:487632/99‑1 (MQ=31)                                    ggCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGGTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCC                  >  1:2064201/3‑101 (MQ=14)                                    cgCGGGGGCTCCCCCCCCGCCCCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCC                  <  2:3781641/99‑1 (MQ=2)                                      CGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGA                <  2:3379154/101‑1 (MQ=1)                                       GGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAG               <  1:2540634/101‑1 (MQ=1)                                       GGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAG               >  2:4254239/1‑101 (MQ=1)                                       GGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGGCTGGAAGCCGAG               >  2:3792155/1‑101 (MQ=1)                                         GGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCT             <  2:1028516/101‑1 (MQ=1)                                         GGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCT             >  2:2022593/1‑101 (MQ=1)                                          tGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTT            <  2:2121190/100‑1 (MQ=1)                                          GGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTT            <  2:3299303/101‑1 (MQ=1)                                          GGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTT            >  2:2834656/1‑101 (MQ=1)                                          GGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTT            >  2:4255640/1‑101 (MQ=1)                                           GCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTa           >  1:2121340/1‑100 (MQ=1)                                            CTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGC          >  2:391647/1‑101 (MQ=1)                                             TCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCC         <  2:1550662/101‑1 (MQ=1)                                             TCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCC         >  2:4385871/1‑101 (MQ=1)                                             TCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCC         >  1:3904558/1‑101 (MQ=1)                                              CCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCC        <  1:3535510/101‑1 (MQ=1)                                               CGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCg       >  2:3855967/1‑100 (MQ=1)                                               CGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCA       <  2:826320/101‑1 (MQ=1)                                                GCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAG      >  1:1894408/1‑101 (MQ=1)                                                GCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAG      >  1:4472112/1‑101 (MQ=1)                                                 CCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGGGCTTGCCCAGC     >  1:4101229/1‑101 (MQ=1)                                                 CCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGC     >  2:3357661/1‑101 (MQ=1)                                                 CCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGC     >  1:2491560/1‑101 (MQ=1)                                                 CCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGC     >  1:560487/1‑101 (MQ=1)                                                   CCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCAC   >  1:1477081/1‑101 (MQ=1)                                                   CCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCAC   >  2:1009168/1‑101 (MQ=1)                                                    CCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCACC  >  2:3211487/1‑101 (MQ=1)                                                    CCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCACC  >  2:2149643/1‑101 (MQ=1)                                              |||||||                                                                                                     GGGGTATTTCGCCTCGGCTGTCGCCGAGGCGACCCGCCGGGGGCT...........................................................................................................  <  NC_014034/974360‑974316 ....................................................CGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCACC  <  NC_014034/1253890‑1253791 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG