New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1395598	212 (1.120)	59 (0.310)	9/130	27.3	0.22	intergenic (+410/‑521)	RCAP_rcc01306/RCAP_rcc01307	Cas2 family CRISPR‑associated protein/hypothetical protein
	?	NC_014034	1397903 =	198 (0.680)					intergenic (+207/+1691)	RCAP_rcc01307/RCAP_rcc01309	hypothetical protein/IS66 family transposase
Rejected: Position hash score below cutoff.

GCCGGCCTGCTCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC...............................................................................  >  NC_014034/1395555‑1395598 ...............................................................................GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCTATGGGAGGC  >  NC_014034/1397903‑1397946                                             |||||||||||||||||||||||||||||||||||                                             tattgcgcGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGT                        <  2:944856/93‑1 (MQ=12) tattgcgcGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGT                        <  1:1283958/93‑1 (MQ=12)  attgcgcGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTG                       >  1:5111761/8‑101 (MQ=12)  attgcgcGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTG                       >  1:1727450/8‑101 (MQ=12)   ttgcgcGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGG                      >  2:4960178/7‑101 (MQ=12)   ttgcgcGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGG                      <  2:3805246/95‑1 (MQ=12)   ttgcgcGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGG                      >  2:1184098/7‑101 (MQ=12)    tgcgcGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGA                     <  1:4474266/96‑1 (MQ=17)     gcgcGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGAT                    <  2:1775035/97‑1 (MQ=17)     gcgcGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGAT                    <  1:4890815/97‑1 (MQ=17)     gcgcGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGAT                    <  1:1028397/97‑1 (MQ=17)      cgcGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATC                   <  1:1890331/98‑1 (MQ=17)       gcGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCG                  >  1:2555406/3‑101 (MQ=17)       gcGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCG                  <  1:1884532/99‑1 (MQ=17)        cGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGA                 <  2:421171/100‑1 (MQ=17)        cGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGA                 <  1:2242879/100‑1 (MQ=17)         GCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                >  1:1270437/1‑101 (MQ=32)         GCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCCAA                >  1:773573/1‑101 (MQ=17)         GCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGCAGCTCCCCCCGCGGGGGCGTGGATCGAA                >  1:552344/1‑101 (MQ=12)          ctgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA               >  1:5776906/4‑101 (MQ=32)           tgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC              <  1:110045/99‑1 (MQ=31)           tgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC              <  2:4029717/99‑1 (MQ=31)           tgGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC              <  1:2735715/99‑1 (MQ=31)           tgGTCGCGCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC              <  2:4795059/99‑1 (MQ=14)            gGTCGCTCCCCCCGCGGGGGCGTGGATCGAGACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACc             >  1:5146556/2‑100 (MQ=11)            gGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACc             >  2:5300578/2‑100 (MQ=11)             GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGGCCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACct            <  2:696738/101‑3 (MQ=1)             GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACct            <  2:5368573/101‑3 (MQ=1)             GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACct            <  2:3035377/101‑3 (MQ=1)              TCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACcta           >  2:789097/1‑98 (MQ=1)              TCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACcta           <  1:4774615/101‑4 (MQ=1)              TCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACcta           >  1:3335354/1‑98 (MQ=1)              TCGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGGGGATCGAAACcta           >  1:5556138/1‑98 (MQ=0)               CGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACctat          >  1:1687567/1‑97 (MQ=1)               CGCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACctat          >  1:4591808/1‑97 (MQ=1)               CGCGCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGACCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACctat          <  2:4955516/101‑5 (MQ=0)                GCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATG        >  1:1576866/1‑101 (MQ=1)                GCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATG        <  1:3168596/101‑1 (MQ=1)                GCTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCCGGGGCGTGGATCGAAAC.CTATG        >  2:724596/1‑101 (MQ=0)                GCTCCCCCCGCGGGGGCGTGGATCGAAAATTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATG        >  2:3747026/1‑101 (MQ=0)                 CTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATGa       <  1:5066891/101‑2 (MQ=0)                 CTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATGa       <  2:2804978/101‑2 (MQ=0)                 CTCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATGa       >  1:1219811/1‑100 (MQ=0)                 CTCCCCCCGCGGGGGCGTGGATCGAAACTTCATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATGa       <  1:372766/101‑2 (MQ=0)                  TCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATGag      <  2:5061920/101‑3 (MQ=0)                  TCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATGag      <  1:973622/101‑3 (MQ=0)                  TCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATGag      >  1:606988/1‑99 (MQ=0)                  TCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATGag      >  1:4546118/1‑99 (MQ=0)                  TCCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATGag      <  1:3528559/101‑3 (MQ=0)                   CCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATGagg     >  2:3987632/1‑98 (MQ=0)                   CCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATGagg     <  1:5421916/101‑4 (MQ=0)                   CCCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCACCCGCGGGGGCGTGGATCGAAAC.CTATGagg     >  2:1794165/1‑98 (MQ=0)                    CCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATGaggg    >  2:3271196/1‑97 (MQ=0)                    CCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATGaggg    <  2:1304492/101‑5 (MQ=0)                    CCCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATGaggg    >  1:813540/1‑97 (MQ=0)                     CCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATGagggc   <  2:3945829/101‑6 (MQ=0)                     CCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATGagggc   <  1:5453605/101‑6 (MQ=0)                     CCCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATGagggc   >  1:4448041/1‑96 (MQ=0)                      CCCGCGGGGGCGTGGATCGAAACTTGATGACCAGATCCGCAATCGGCCGGGCTCGATCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC.CTATGagggct  >  2:4027802/1‑95 (MQ=0)                                             |||||||||||||||||||||||||||||||||||                                             GCCGGCCTGCTCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC...............................................................................  >  NC_014034/1395555‑1395598 ...............................................................................GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTCTATGGGAGGC  >  NC_014034/1397903‑1397946 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 26 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG