New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	974316 =	1 (0.010)	42 (0.220)	7/182	26.4	0.76	intergenic (+196/+63)	RCAP_rcc00884/RCAP_rcc00885	hypothetical protein/hypothetical protein
	?	NC_014034	= 1253890	25 (0.120)					intergenic (+48/+43)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
Rejected: Position hash score below cutoff.

GGGTATTTCGCCTCGGCTGTCGCCGAGGCGACCCGCCGGGGGCT..........................................................................................................  <  NC_014034/974359‑974316 ...................................................CGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCAC  <  NC_014034/1253890‑1253792                                             |||||||                                                                                                    gaggATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTT                                                   <  1:207399/97‑1 (MQ=32)  gggATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTA                                                  <  1:2539774/98‑1 (MQ=17)  aggATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTA                                                  <  1:3904326/98‑1 (MQ=32)    gATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATT                                                <  2:398008/100‑1 (MQ=32)      TTTCCCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTC                                              <  1:964550/101‑1 (MQ=17)         CGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCC                                           <  2:1675891/101‑1 (MQ=32)          GCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCT                                          <  1:3876801/101‑1 (MQ=32)           CCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTC                                         <  1:3905976/101‑1 (MQ=32)            CTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCG                                        <  2:1309551/101‑1 (MQ=32)            CTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCG                                        <  2:106327/101‑1 (MQ=32)            CTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCG                                        <  2:4012738/101‑1 (MQ=32)             TCGGCTTTCGCCGAGGCGCCCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGA                                       <  2:3740972/101‑1 (MQ=17)               GGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAG                                     <  1:3502045/101‑1 (MQ=32)                GCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGG                                    <  2:2891671/101‑1 (MQ=32)                GCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGG                                    <  1:3672838/101‑1 (MQ=32)                 cttTCGCCGAGGCGCCCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGC                                   <  2:241733/98‑1 (MQ=17)                    TCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCA                                <  2:3710606/101‑1 (MQ=32)                    TCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCA                                <  2:1178416/101‑1 (MQ=32)                    TCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCA                                <  1:1361993/101‑1 (MQ=32)                     CGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAG                               <  1:88677/101‑1 (MQ=32)                     CGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAG                               <  1:1134001/101‑1 (MQ=32)                      GCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGC                              <  2:1528949/101‑1 (MQ=32)                         GAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGG                           <  2:2189547/101‑1 (MQ=32)                              gcCCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCCCAGCCGGTCTGG                      <  1:2291658/99‑1 (MQ=17)                              gcCCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGAGCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGG                      <  1:2042278/99‑1 (MQ=17)                                CCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAA                    <  1:3849256/101‑1 (MQ=32)                                 CCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAG                   <  1:1995106/101‑1 (MQ=32)                                  cggCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGC                  <  2:4211921/98‑1 (MQ=32)                                    gCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCG                <  1:1317538/100‑1 (MQ=11)                                    gCGGGGACTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCG                <  2:3856971/100‑1 (MQ=11)                                     gGGGGGCCCCCCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGA               <  1:1460698/100‑1 (MQ=0)                                      GGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGGCTCGAAGGAGCAGCCGGTCTGGGAGCCGAG              >  2:1664232/1‑101 (MQ=0)                                      GGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAG              >  2:2159290/1‑101 (MQ=1)                                      GGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAG              >  2:1127441/1‑101 (MQ=1)                                       GGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGC             <  1:50021/101‑1 (MQ=1)                                         GGCTCCGCCCCCGCCCCCCCGAGGTATTTAGGGCAAGATAAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTT           <  2:779777/101‑1 (MQ=0)                                         GGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCCAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTT           <  1:3634017/101‑1 (MQ=1)                                         GGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGccctt           <  2:3582048/101‑6 (MQ=1)                                         GGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTT           >  2:3216606/1‑101 (MQ=1)                                         GGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTT           <  1:4049554/101‑1 (MQ=1)                                          GCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTG          <  1:212548/101‑1 (MQ=1)                                          GCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTG          <  2:1534348/101‑1 (MQ=1)                                            cCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCC        <  2:1758546/100‑1 (MQ=1)                                            TCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCC        >  1:2679440/1‑101 (MQ=1)                                             CCGCCCCCGCCCCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCC       <  1:3080398/101‑1 (MQ=1)                                              CGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCA      <  2:3186399/101‑1 (MQ=1)                                              CGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCA      <  1:2931106/101‑1 (MQ=1)                                              CGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCA      <  1:2337399/101‑1 (MQ=1)                                                CCCCCGCACCCCCGAGGTATTTAGGGCAAGATGTGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGC    <  1:3624506/101‑1 (MQ=1)                                                 CCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCA   <  1:2640140/101‑1 (MQ=1)                                                 CCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCA   <  2:3794108/101‑1 (MQ=1)                                                  CCCGCACCCCCGAGGTATTTAGGGCAAGAGGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCAC  <  2:773657/101‑1 (MQ=1)                                             |||||||                                                                                                    GGGTATTTCGCCTCGGCTGTCGCCGAGGCGACCCGCCGGGGGCT..........................................................................................................  <  NC_014034/974359‑974316 ...................................................CGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCAC  <  NC_014034/1253890‑1253792 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG