New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	974316 =	1 (0.000)	39 (0.190)	9/182	27.7	0.77	intergenic (+196/+63)	RCAP_rcc00884/RCAP_rcc00885	hypothetical protein/hypothetical protein
	?	NC_014034	= 1253890	22 (0.100)					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 ....................................................CGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCAC  <  NC_014034/1253890‑1253792                                              |||||||                                                                                                    agaggATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTT                                                    <  2:3266944/96‑1 (MQ=32) agaggATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTT                                                    <  2:3242456/96‑1 (MQ=32)    ggATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTAT                                                 <  2:4045528/99‑1 (MQ=32)       TTTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTC                                              <  2:627028/101‑1 (MQ=32)        TTCGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCG                                             <  2:4104994/101‑1 (MQ=32)          CGCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCC                                           <  1:275792/101‑1 (MQ=32)           nCCNCNNCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCT                                          <  1:2086205/100‑1 (MQ=17)           GCCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCT                                          <  1:2571493/101‑1 (MQ=32)            CCTCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTC                                         <  2:4061283/101‑1 (MQ=32)              TCGGCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGA                                       <  1:3610411/101‑1 (MQ=32)                 GCTTTCGCCGAGGCGACCCGGCGGGGGCTCCGCTCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGG                                    <  1:3801039/101‑1 (MQ=32)                   ttTCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCG                                  <  1:3978141/99‑1 (MQ=32)                     TCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCA                                <  1:106824/101‑1 (MQ=32)                         CGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCG                            <  2:4087145/101‑1 (MQ=32)                          GAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGG                           <  1:2332204/101‑1 (MQ=32)                             GCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCT                        <  1:3919943/101‑1 (MQ=32)                              CGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTG                       <  1:2299014/101‑1 (MQ=32)                               GACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGG                      <  2:3607159/101‑1 (MQ=32)                                  CCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAG                   <  1:2923627/101‑1 (MQ=32)                                   cggCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGC                  <  2:2106422/98‑1 (MQ=32)                                   cggCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGC                  <  1:3076247/98‑1 (MQ=32)                                     gCGGGGGCTCCGCCCCCGCCCCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCG                <  2:1656170/100‑1 (MQ=11)                                     gCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCG                <  2:2278980/100‑1 (MQ=11)                                       GGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAG              >  2:2663262/1‑101 (MQ=1)                                       GGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAG              >  2:511076/1‑101 (MQ=1)                                       GGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAG              <  1:548740/101‑1 (MQ=1)                                       GGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAG              >  2:3656738/1‑101 (MQ=1)                                       GGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAG              >  1:3929850/1‑101 (MQ=1)                                       GGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAG              <  1:2736690/101‑1 (MQ=1)                                       GGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGGCTGGAAGCCGAG              >  2:3259412/1‑101 (MQ=1)                                        GGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGC             <  2:1276243/101‑1 (MQ=1)                                        GGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGC             >  2:2798068/1‑101 (MQ=1)                                         GGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCT            >  2:1308890/1‑101 (MQ=1)                                         GGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCT            >  2:1055339/1‑101 (MQ=1)                                          GGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTT           >  2:2147067/1‑101 (MQ=1)                                          GGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTT           >  1:4206463/1‑101 (MQ=1)                                          GGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGATT           >  2:2655417/1‑101 (MQ=1)                                           GCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTG          >  2:1137939/1‑101 (MQ=1)                                           GCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTG          <  2:3477162/101‑1 (MQ=1)                                             TCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGGCGAGCTTGCC        >  2:3127795/1‑101 (MQ=1)                                             TCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCC        >  2:1676101/1‑101 (MQ=1)                                             TCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCC        >  1:3086969/1‑101 (MQ=1)                                              CCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCC       >  1:2175364/1‑101 (MQ=1)                                               CGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCA      >  1:304345/1‑101 (MQ=1)                                               CGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCA      >  1:99134/1‑101 (MQ=1)                                               CGCCCCCGCACCCCCGAGGGATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGGCTGGAAGCCGAGCTTGCCCA      >  1:2716882/1‑101 (MQ=0)                                                 CCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGC    >  2:53212/1‑101 (MQ=1)                                                 CCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGC    >  1:2059956/1‑101 (MQ=1)                                                  CCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCA   >  1:1981245/1‑101 (MQ=1)                                                  CCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCA   >  2:2829588/1‑101 (MQ=1)                                                  CCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCA   <  2:2554340/101‑1 (MQ=1)                                                   CCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCAC  >  2:1482646/1‑101 (MQ=1)                                                   CCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCAC  <  1:3004662/101‑1 (MQ=1)                                              |||||||                                                                                                    GGGGTATTTCGCCTCGGCTGTCGCCGAGGCGACCCGCCGGGGGCT..........................................................................................................  <  NC_014034/974360‑974316 ....................................................CGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCAC  <  NC_014034/1253890‑1253792 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG