New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1395633 =	128 (0.930)	42 (0.310)	13/130	16.6	0.24	intergenic (+445/‑486)	RCAP_rcc01306/RCAP_rcc01307	Cas2 family CRISPR‑associated protein/hypothetical protein
	?	NC_014034	= 1396738	144 (0.680)					coding (620/1578 nt)	RCAP_rcc01307	hypothetical protein
Rejected: Position hash score below cutoff.

GTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGCGGCTCGAACTGCCCGCCGACTACATGCAGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC................................................................................  <  NC_014034/1395730‑1395633 .....................................................................................................................................GGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATGACGGATCG  <  NC_014034/1396738‑1396694                                                                                                   |||||||||||||||||||||||||||||||||||                                              GTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGCGGCTCGAACTGCCCGCCGACTACATGCAGATGTTTCGATCCACGCCCCCCCGGGGGGGGCGACCct                                                                               >  2:853172/1‑99 (MQ=0)                                                      cggtcaagctGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGC                          >  1:2475665/11‑101 (MQ=16)                                                        gtcaagctGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGGCCTCATAGGTTTCGATCCACGCCCCCGCGG                        >  2:38907/9‑101 (MQ=16)                                                         tcaagctGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGG                       >  1:3736459/8‑101 (MQ=18)                                                           aagctGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGG                     <  1:877473/96‑1 (MQ=18)                                                            agctGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGG                    <  2:2389395/97‑1 (MQ=33)                                                            agctGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGG                    >  1:162541/5‑101 (MQ=33)                                                             gctGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGA                   <  1:2246081/98‑1 (MQ=32)                                                             gctGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGA                   <  2:1754110/98‑1 (MQ=32)                                                               tGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGGGC                 >  1:4474/2‑101 (MQ=11)                                                               tGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGCGC                 >  2:3236630/2‑101 (MQ=11)                                                               tGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGC                 >  1:2476252/2‑101 (MQ=11)                                                               tGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGC                 <  1:632701/100‑1 (MQ=11)                                                                GATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCG                <  2:448201/101‑1 (MQ=1)                                                                GATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCG                <  2:1806113/101‑1 (MQ=1)                                                                 ATGTTTCGATCCCCGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGA               <  1:1181134/101‑1 (MQ=1)                                                                  TGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGTGAC              >  1:3797446/1‑101 (MQ=1)                                                                  TGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC              <  1:2729630/101‑1 (MQ=1)                                                                   GTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACG             <  2:2306886/101‑1 (MQ=1)                                                                   GTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACG             >  1:2016934/1‑101 (MQ=1)                                                                    TTTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGA            >  2:1052830/1‑101 (MQ=1)                                                                     TTCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGAT           <  1:1854199/101‑1 (MQ=1)                                                                     TTCGACCCCCGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGAT           <  1:42687/101‑1 (MQ=0)                                                                      TCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATc          <  2:2944841/101‑2 (MQ=1)                                                                      TCGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCAACGACCGGGCCGCCAGCCCTCATAGGATTCGATCCACGTCCCCGCGGGGGGAGCGACGATG          >  2:3165394/1‑101 (MQ=0)                                                                       CGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATcg         >  2:4150910/1‑99 (MQ=1)                                                                       CGATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATcg         <  1:3087753/101‑3 (MQ=1)                                                                        GATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATCGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATcga        >  1:2672350/1‑98 (MQ=0)                                                                        GATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATcga        >  2:1766922/1‑98 (MQ=1)                                                                        GATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATcga        >  1:3930233/1‑98 (MQ=1)                                                                         ATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATcgag       >  1:1184727/1‑97 (MQ=1)                                                                         ATCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATcgag       >  2:54917/1‑97 (MQ=1)                                                                          TCCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGGGCGACGATcgagc      >  2:2341545/1‑96 (MQ=0)                                                                           cccCGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATcgagcc     <  1:3226153/98‑7 (MQ=0)                                                                           CCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATcgagcc     <  1:3549763/101‑7 (MQ=0)                                                                           CCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATcgagcc     >  1:675236/1‑95 (MQ=0)                                                                           CCACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATcgagcc     >  1:1908074/1‑95 (MQ=0)                                                                            CACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATcgagccc    >  2:2956261/1‑94 (MQ=0)                                                                            CACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATcgagccc    <  2:3260950/101‑8 (MQ=0)                                                                            CACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATcgagccc    <  2:4157795/101‑8 (MQ=0)                                                                            CACGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATcgagccc    >  2:842847/1‑94 (MQ=0)                                                                              CGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATcgagcgaca  <  2:3797186/101‑10 (MQ=0)                                                                              CGCCCCCGCGGGGGGAGCGACCGGCGGGATCCACGACCGGGCCGCCAGCCCTCATAGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATcgagcccgg  >  2:3615540/1‑92 (MQ=0)                                                                                                   |||||||||||||||||||||||||||||||||||                                              GTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGCGGCTCGAACTGCCCGCCGACTACATGCAGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC................................................................................  <  NC_014034/1395730‑1395633 .....................................................................................................................................GGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATGACGGATCG  <  NC_014034/1396738‑1396694 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 24 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG