New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1396099 =	128 (0.830)	68 (0.440)	11/130	18.2	0.32	intergenic (+911/‑20)	RCAP_rcc01306/RCAP_rcc01307	Cas2 family CRISPR‑associated protein/hypothetical protein
	?	NC_014034	= 1396401	155 (0.650)					coding (283/1578 nt)	RCAP_rcc01307	hypothetical protein
Rejected: Position hash score below cutoff.

ATGACGAAAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC.................................................................................  <  NC_014034/1396140‑1396099 .............................................................................GTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGCGTTTGTCTGGT  <  NC_014034/1396401‑1396356                                           |||||||||||||||||||||||||||||||||||                                               tcgaggccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGG                        <  2:684213/92‑1 (MQ=21) tcgaggccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGG                        <  1:2357086/92‑1 (MQ=21)  cgaggccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGa                       >  1:684277/9‑100 (MQ=18)  cgaggccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGG                       >  1:4146116/9‑101 (MQ=18)  cgaggccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGG                       >  1:2505007/9‑101 (MQ=18)   gaggccggGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGG                      >  2:1725470/9‑101 (MQ=17)   gaggccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGG                      >  1:2159914/8‑101 (MQ=17)    aggccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGGGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGA                     <  1:1468121/95‑1 (MQ=9)    aggccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGg                     >  1:1000110/7‑100 (MQ=14)    aggccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGA                     <  2:1726268/95‑1 (MQ=14)     ggccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGgg                    >  2:3862502/6‑99 (MQ=11)     ggccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAG                    >  2:4465160/6‑101 (MQ=11)     ggccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAG                    >  2:3733892/6‑101 (MQ=11)      gccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGGGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGCGC                   >  1:1324092/5‑101 (MQ=2)      gccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGC                   >  1:3065801/5‑101 (MQ=11)      gccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGC                   <  2:3613733/97‑1 (MQ=11)      gccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGC                   <  1:3969387/97‑1 (MQ=11)       ccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCG                  >  2:519228/4‑101 (MQ=14)       ccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCG                  <  1:1440715/98‑1 (MQ=14)       ccgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCG                  <  2:1789389/98‑1 (MQ=14)        cgAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGA                 <  2:2521528/99‑1 (MQ=31)         gAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC                >  1:3162291/2‑101 (MQ=11)         gAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC                <  2:3054506/100‑1 (MQ=11)         gAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC                <  1:3769728/100‑1 (MQ=11)          tcTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACA               <  1:2091579/99‑1 (MQ=1)          AGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACA               <  1:163142/101‑1 (MQ=1)          AGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACA               >  2:4389553/1‑101 (MQ=1)          AGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACA               <  2:3341761/101‑1 (MQ=1)          AGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACA               <  2:3866929/101‑1 (MQ=1)          AGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACA               >  2:364363/1‑101 (MQ=1)          AGTTTCGATCCACGCCACCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACA               <  2:1324000/101‑1 (MQ=1)           GTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAG              <  1:2421597/101‑1 (MQ=1)           GTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAG              <  2:3294759/101‑1 (MQ=1)           GTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAG              <  1:3794378/101‑1 (MQ=1)            TTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGt             <  2:2757744/101‑2 (MQ=1)            TTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGt             <  2:367611/101‑2 (MQ=1)             TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCGGACAAAGATCCGTCGCGGCGCGCGCCAGCGTTTCGATCGACGCCCCCGCGGGGGGAGCGACAGtg            >  2:1537462/1‑99 (MQ=0)             TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAaga            >  2:2091458/1‑98 (MQ=1)             TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGtg            <  1:1234552/101‑3 (MQ=1)             TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGtg            >  1:550018/1‑99 (MQ=1)             TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGtg            >  2:4401029/1‑99 (MQ=1)              TCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGGGCGACcgtgt           >  2:1715945/1‑96 (MQ=0)              TCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGT           <  2:2395214/101‑1 (MQ=1)               CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTT          >  1:3070719/1‑101 (MQ=1)               CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTT          <  2:1380891/101‑1 (MQ=1)               CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTT          <  1:2689009/101‑1 (MQ=1)               CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTT          <  2:2775942/101‑1 (MQ=1)                GATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTg         >  2:1669496/1‑100 (MQ=1)                GATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCAATCCACGCCCCCGCGGGGGGAGCGACAGTGTTg         >  1:4087114/1‑100 (MQ=0)                 ATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTga        <  1:1142741/101‑3 (MQ=1)                 ATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTga        >  2:2323403/1‑99 (MQ=1)                 ATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTga        <  2:2662702/101‑3 (MQ=1)                 ATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTga        <  2:2472358/101‑3 (MQ=1)                 ATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTga        >  1:3310514/1‑99 (MQ=1)                  TCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTgac       <  1:955449/101‑4 (MQ=0)                   CCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTgacc      >  1:3237825/1‑97 (MQ=0)                   CCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTgacc      >  2:4249747/1‑97 (MQ=0)                    CACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTgacca     <  1:475159/101‑6 (MQ=0)                     cCGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTgaccac    <  1:4033887/100‑7 (MQ=0)                     ACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTgaccac    <  2:2093478/101‑7 (MQ=0)                     ACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTgaccac    >  2:346820/1‑95 (MQ=0)                     ACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTgaccac    <  1:3416150/101‑7 (MQ=0)                     ACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTgaccac    >  2:385988/1‑95 (MQ=0)                     ACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTgaccac    <  1:784051/101‑7 (MQ=0)                     ACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTgaccac    <  1:4130066/101‑7 (MQ=0)                      CGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTgaccaca   >  2:179084/1‑94 (MQ=0)                      CGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTgaccaca   <  1:4582085/101‑8 (MQ=0)                       GCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGTGTTgaccacat  <  1:3664871/101‑9 (MQ=0)                                           |||||||||||||||||||||||||||||||||||                                               ATGACGAAAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC.................................................................................  <  NC_014034/1396140‑1396099 .............................................................................GTTTCGATCCACGCCCCCGCGGGGGGAGCGACAGCGTTTGTCTGGT  <  NC_014034/1396401‑1396356 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG