New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1253890	33 (0.160)	24 (0.120)	3/192	31.0	0.38	intergenic (+48/+43)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
	?	NC_014034	= 1721531	45 (0.210)					intergenic (‑426/+20)	RCAP_rcc01588/RCAP_rcc01589	GSCFA family protein/ErfK/YbiS/YcfS/YnhG family protein
Rejected: Position hash score below cutoff.

GGGCCTCCCTCCCGCAGCGCTTTATTTTTGGCC.GG.TCGCCTTGGGGATTT.CGCCTCGGCTGCGCCGAGGCGACCCGCC....GGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCAGCC  >  NC_014034/1721442‑1721631                                                                                                 |                                                                                                     gggCCTCCCTCCCGCAGCGCTTTATTTTTGGCC.GG.TCGCCTTGGGGATTT.CGCCTCGGCTGCGCCGAGGCGACCCGCCCG..GGGCCGGGCCCCCCGGccccc                                                                                             >  2:2699279/1‑101 (MQ=25)   gCCTCCCTCCCGCAGCGCTTTATTTTTGGCC.GG.TCGCCTTGGGGATTT.CGCCTCGGCTGCGCCGAGGCGACCCGCCGG..GGGGTGGGCCCCCCGGccccccc                                                                                           >  2:2024375/1‑101 (MQ=25)       cccccccGCGTCGTTTTTTTTTTGGCG.GG.CCCCCTGGGGTTTTC.CGCCCCGGCCCCCCCGGGGCCCCCCGCCGG..GGGCTGCGCCCCCGGACCCCCCCCGaa                                                                                       <  1:1998221/101‑1 (MQ=2)         ctcccGCAGCGCTTTATTTTTGGCC.GG.TCGCCTTGGGGATTT.CGCCTCGGCTGCGCCGAGGCGACCCGCCGG..GGGCTGGGCCCCCGGACCCCCCCCGCAGa                                                                                     >  2:537195/1‑101 (MQ=21)         ctcccGCAGCGCTTTATTTTTGGCC.GG.TCGCCTTGGGGATTT.CGCCTCGGCTGCGCCGAGGCGACCCGCCGG..GGGCGGCGCCCCCGGGccccccccccaga                                                                                     >  2:2471561/1‑96 (MQ=21)          ccccGCGGCTTTTTTTTTTGGGCC.GG..CCCCTTGGGGGTTTCCCCCGCGGCCGCGCCGGGGCCCCCCGCCGG..GGGCTGCGCCCCCGGACCCCCCCCGAAGAt                                                                                    <  1:2472855/100‑1 (MQ=9)             cGCAGCGCTTTATTTTTGGCC.GG.TCGCCTTGGGGATTT.CGCCTCGGCTGCGCCGAGGCGACCCGCCCGGGGGGGGGCGCCCCCGGCccccccccccccatc                                                                                   >  1:1393939/1‑94 (MQ=21)                 ggtttttTTTTTGGGCC.GG.CCTCCGGGGGGTTTC.CCCCTGGGCCGCGCAGGGGCGCCCCGCCGG..GGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGAt                                                                             <  1:1288228/97‑1 (MQ=255)                 cgtttttTTTTTTGGGC.GGTTCGCTTTGGGGTTTC.CCCCGCGGCGCCCCCGGGGCCCCCCGCCGG..GGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGa                                                                              <  1:3416447/97‑1 (MQ=9)                    cTTTATTTTTGGCC.GG.TCGCCTTGGGGATTT.CGCCTCGGCTGCGCCGAGGCGACCCGCCGG..GGGCTGCGCCCCCCGACCCCCCCCGAAGATCTCAGATCAc                                                                          >  2:2065036/1‑101 (MQ=25)                       tttttttGGCCGGG.TGGGTTTGGGGTTTT.CGCCGCGGCCGCGCCGGGCCCCCCCGCCGG..GGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCt                                                                        <  2:3891594/99‑1 (MQ=12)                          ttgtGGCC.GC.TCGCGTTGGCGTTTC.CGCCGGGGCGGCGCGGAGGCCCCCCGCCGG..GGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGAc                                                                    <  2:255739/98‑1 (MQ=255)                              ggCG.GG.TCGCCTGGGGGTTCC.CGCCCGGGCGGCCCCGGGCCGCCCCGCCGG..GGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGc                                                                <  1:2699485/101‑1 (MQ=255)                                              gggttttccGCCGCGGCCGCGCGGAGGCCCCCCGCCGG..GGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGc                                                   <  1:4217529/93‑1 (MQ=21)                                                     ccGCCGCGGCGGCCCCGAGGCCCCCCGCCGG..GGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCgg                                            <  2:3426966/100‑1 (MQ=255)                                                             gCTGCGCCGAGGCGACCCGCCGG..GGGCTGGGCCCCCGGACCCCCCCCCCAGAACTCAGATAACCCTGGCCTCCGTGCCGCCCGGGCAGAGCGGACAAAggt                                    >  1:1908908/1‑99 (MQ=12)                                                                            cgcccgccgggggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGc                       <  1:2706171/91‑1 (MQ=255)                                                                               ccgccgggggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCAtt                    <  1:3329004/94‑1 (MQ=255)                                                                                 gccgggggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGa                  <  2:694109/96‑1 (MQ=255)                                                                                 cccgggagCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGa                  <  1:689600/94‑1 (MQ=255)                                                                                  ccgggggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGaa                 <  2:1942844/97‑1 (MQ=255)                                                                                     ggggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAg              >  1:2662510/2‑101 (MQ=255)                                                                                     ggggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCCGCGTGGCGCCCGGGCCGAGCGGATAAAGGTCCTCGACCTGGGCGTTGAACAg              >  2:2990827/2‑101 (MQ=255)                                                                                      gggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGt             >  2:2316191/1‑101 (MQ=255)                                                                                       ggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTc            >  1:2047778/1‑101 (MQ=255)                                                                                       ggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTc            >  1:312089/1‑101 (MQ=255)                                                                                       ggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTc            >  2:3604181/1‑101 (MQ=255)                                                                                       ggCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTc            >  1:2704233/1‑101 (MQ=255)                                                                                         cTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCg          >  2:1729646/1‑101 (MQ=255)                                                                                         cTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCg          <  2:713530/101‑1 (MQ=255)                                                                                         cTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCg          <  2:631538/101‑1 (MQ=255)                                                                                         cTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGCGCCGACCGGGCAGAGCGGAAAAAGTTCCTCGACCGGGGCATTGAACAgccag          >  2:4147944/1‑97 (MQ=255)                                                                                          tGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGa         >  1:1316386/1‑101 (MQ=255)                                                                                          tGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGa         <  2:343065/101‑1 (MQ=255)                                                                                           gcgcCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCTGATTAAGTTCCTCGACCTGGGCATTGAACAGTCCGAt        >  1:3620982/1‑101 (MQ=255)                                                                                           gcgcCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGAt        <  2:2787276/101‑1 (MQ=255)                                                                                           gcgcCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGAt        <  2:763240/101‑1 (MQ=255)                                                                                            cgcCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATg       >  2:3730316/1‑101 (MQ=255)                                                                                            cgcCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATg       <  2:686609/101‑1 (MQ=255)                                                                                            cccccccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATg       <  1:4105944/99‑1 (MQ=255)                                                                                             gcCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGc      <  1:893828/101‑1 (MQ=255)                                                                                             gcCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGc      <  2:768941/101‑1 (MQ=255)                                                                                               ccccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCAg    <  1:82473/101‑1 (MQ=255)                                                                                                cccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCAGc   >  1:960466/1‑101 (MQ=255)                                                                                                 ccGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCAGcc  >  2:2807989/1‑101 (MQ=255)                                                                                                 |                                                                                                     GGGCCTCCCTCCCGCAGCGCTTTATTTTTGGCC.GG.TCGCCTTGGGGATTT.CGCCTCGGCTGCGCCGAGGCGACCCGCC....GGGCTGCGCCCCCGGACCCCCCCCGAAGATCTCAGATCACCTTGACCTGCGTGCCGACCGGGCAGAGCGGATAAAGTTCCTCGACCTGGGCATTGAACAGTCCGATGCAGCC  >  NC_014034/1721442‑1721631 Base quality scores:  ATCG  < 3 ≤  ATCG  < 16 ≤  ATCG  < 27 ≤  ATCG  < 34 ≤  ATCG  < 41 ≤  ATCG