New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1395665	179 (1.160)	60 (0.390)	10/130	18.9	0.26	intergenic (+477/‑454)	RCAP_rcc01306/RCAP_rcc01307	Cas2 family CRISPR‑associated protein/hypothetical protein
	?	NC_014034	1397034 =	161 (0.680)					coding (916/1578 nt)	RCAP_rcc01307	hypothetical protein
Rejected: Position hash score below cutoff.

CGCGGGGCGAAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACA....................................................................................................................................  >  NC_014034/1395620‑1395665 .................................................................................GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTGCCGTCTTGAGTGATGGGGCGCGAGCACATGTCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA  >  NC_014034/1397034‑1397130                                               |||||||||||||||||||||||||||||||||||                                                                                                  ggcgccatcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGC                                                                               <  2:2337909/91‑1 (MQ=0) agctccatcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGC                                                                               <  1:778089/91‑1 (MQ=0) agcgccatcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGC                                                                               <  2:344807/91‑1 (MQ=0) agcgccatcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGC                                                                               <  2:1377013/91‑1 (MQ=0)  gcgccatcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCG                                                                              <  1:4385259/92‑1 (MQ=0)   cgccatcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGT                                                                             <  1:3114525/93‑1 (MQ=0)   cgccatcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGT                                                                             <  1:1550738/93‑1 (MQ=0)   cgccatcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGT                                                                             <  2:2343916/93‑1 (MQ=0)    gccatcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTG                                                                            <  2:1584295/94‑1 (MQ=0)     ccatcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGG                                                                           >  1:1694343/7‑101 (MQ=0)     ccatcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGG                                                                           <  2:1147668/95‑1 (MQ=0)     ccatcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGG                                                                           <  1:806117/95‑1 (MQ=0)     ccatcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGG                                                                           <  2:3888619/95‑1 (MQ=0)      catcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGg                                                                          >  2:3250172/6‑100 (MQ=0)      catcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGA                                                                          <  1:474529/96‑1 (MQ=1)       atcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGAT                                                                         <  2:2583557/97‑1 (MQ=1)       atcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGAT                                                                         >  2:1412737/5‑101 (MQ=1)       atcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGAT                                                                         >  2:2856420/5‑101 (MQ=1)       atcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGAT                                                                         <  1:234407/97‑1 (MQ=1)       atcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGAT                                                                         <  1:1152879/97‑1 (MQ=1)        tcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATC                                                                        <  1:1763941/98‑1 (MQ=1)        tcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATC                                                                        >  1:4320376/4‑101 (MQ=1)        tcgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATC                                                                        <  2:3922464/98‑1 (MQ=1)         cgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCG                                                                       >  2:2500938/3‑101 (MQ=1)         cgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCG                                                                       <  2:1368405/99‑1 (MQ=1)         cgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCG                                                                       >  2:1094777/3‑101 (MQ=1)         cgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCG                                                                       >  1:3916306/3‑101 (MQ=1)         cgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCG                                                                       >  1:3779748/3‑101 (MQ=1)         cgAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCACCCCGCGGGGGCGTGGAGCG                                                                       >  2:595788/3‑101 (MQ=0)          gAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGA                                                                      >  1:1227347/2‑101 (MQ=1)          gAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGA                                                                      >  2:1944525/2‑101 (MQ=1)           AGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                                                                     >  2:495057/1‑101 (MQ=1)           AGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                                                                     <  1:2839753/101‑1 (MQ=1)            GCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA                                                                    <  2:2860061/101‑1 (MQ=1)            GCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA                                                                    <  1:4127270/101‑1 (MQ=1)            GCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA                                                                    <  1:3785439/101‑1 (MQ=1)            GCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGGGGATCGAAA                                                                    >  2:3968801/1‑101 (MQ=1)             CGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC                                                                   >  1:3507245/1‑101 (MQ=1)             CGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC                                                                   <  1:190012/101‑1 (MQ=1)              GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACa                                                                  >  2:847278/1‑100 (MQ=1)              GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACa                                                                  >  1:2982931/1‑100 (MQ=1)              GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACa                                                                  >  1:294467/1‑100 (MQ=1)               TCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGGTCGAAACaa                                                                 >  1:4295948/1‑99 (MQ=1)               TCGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGGGGATCGAAACaa                                                                 >  1:297568/1‑99 (MQ=1)                CGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaaa                                                                >  1:717802/1‑98 (MQ=1)                CGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaaa                                                                >  2:3931156/1‑98 (MQ=1)                CGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaaa                                                                <  1:1252647/101‑4 (MQ=1)                CGCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaaa                                                                >  1:2841537/1‑98 (MQ=1)                CGCGCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaaa                                                                <  1:80453/101‑4 (MQ=1)                CGCCCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaaa                                                                <  2:4499054/101‑4 (MQ=1)                 GCTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaaaa                                                               <  1:2129493/101‑5 (MQ=1)                  CTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaaaaa                                                              <  1:1532140/101‑6 (MQ=1)                  CTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaaaaa                                                              <  2:2679666/101‑6 (MQ=1)                  CTCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaaaaa                                                              <  2:2640752/101‑6 (MQ=1)                   TCCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaaaaag                                                             >  2:2120099/1‑95 (MQ=1)                    CCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaaaaagc                                                            <  2:2064852/101‑8 (MQ=0)                    CCCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaaaaagc                                                            >  1:596667/1‑94 (MQ=0)                     CCCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaaaaagcc                                                           >  2:4235921/1‑93 (MQ=0)                      CCCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaaaaagccg                                                          >  2:2576132/1‑92 (MQ=0)                       CCCGCGGGGGCGTGGATCGAAACACCAATGCCGAAGCCAAGGCCGCAGCAGCGGCTGCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACaaaaagccgc                                                         <  2:301723/101‑11 (MQ=0)                                                                              cgtGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTGCCGTCTTGAGTGATGGGGCGCGAGCACATGCCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA  >  1:3202377/4‑101 (MQ=11)                                               |||||||||||||||||||||||||||||||||||                                                                                                  CGCGGGGCGAAGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACA....................................................................................................................................  >  NC_014034/1395620‑1395665 .................................................................................GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACTGCCGTCTTGAGTGATGGGGCGCGAGCACATGTCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA  >  NC_014034/1397034‑1397130 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 24 ≤  ATCG  < 33 ≤  ATCG  < 38 ≤  ATCG