New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1397903 =	147 (0.920)	45 (0.280)	3/130	22.9	0.20	intergenic (+207/+1691)	RCAP_rcc01307/RCAP_rcc01309	hypothetical protein/IS66 family transposase
	?	NC_014034	= 1434381	224 (0.910)					intergenic (‑160/‑798)	RCAP_rcc01334/RCAP_rcc01335	hypothetical protein/Fis family GAF modulated sigma54 specific transcriptional regulator
Rejected: Position hash score below cutoff.

TCCCATAGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC..............................................................................  <  NC_014034/1397943‑1397903 ............................................................................GTTTCGATCCACGCCCCCGCGGGGGGAGCGACCCAGCAGGATC  <  NC_014034/1434381‑1434339                                          |||||||||||||||||||||||||||||||||||                                            ccctcatagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGG                    >  2:1326626/10‑101 (MQ=0) ccctcatagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGG                    <  2:3725007/92‑1 (MQ=0)  cctcatagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGGTTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGG                   >  1:4244618/9‑101 (MQ=0)  cctcatagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGG                   >  2:1394814/9‑101 (MQ=0)  cctcatagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGG                   <  1:4037226/93‑1 (MQ=0)   ctcatagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGg                  >  2:4937241/8‑100 (MQ=0)   ctcatagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGA                  <  2:3106645/94‑1 (MQ=0)   ctcatagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGA                  <  1:2439499/94‑1 (MQ=0)   ctcatagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGA                  >  1:3037247/8‑101 (MQ=0)   ctcatacGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGA                  >  1:2066794/8‑101 (MQ=0)    tcatagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAG                 >  1:4987852/7‑101 (MQ=0)     catagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGC                <  2:3416623/96‑1 (MQ=1)     catagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGC                <  1:4871950/96‑1 (MQ=1)     catagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGC                >  1:3994964/6‑101 (MQ=1)     catagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGC                <  1:378423/96‑1 (MQ=1)     catagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGC                <  1:3715007/96‑1 (MQ=1)     catagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGC                >  1:155601/6‑101 (MQ=1)     catagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGC                >  2:5007659/6‑101 (MQ=1)     catagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGC                >  1:1057341/6‑101 (MQ=1)      atagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCG               >  1:4949381/5‑101 (MQ=1)      atagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCG               >  2:4289950/5‑101 (MQ=1)      atagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACACCCCCGCGGGGGGAGCG               >  2:4539446/5‑101 (MQ=0)      atagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGGCATCAAGTTTCGATCCACGCCCCCGCGGGGGGGGCG               >  2:2876833/5‑101 (MQ=0)       tagGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCCAGCCCGGCCGATTGCGGATTTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGc              >  1:4264405/4‑100 (MQ=0)        agGTTTCGATCCCCGCCCCCGCGGGGGGAGCGCCGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC             <  2:4754906/99‑1 (MQ=0)        agGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC             >  2:4361923/3‑101 (MQ=1)        agGTTGCGAGCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC             <  2:1077901/99‑1 (MQ=0)         gGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACC            <  2:3711699/100‑1 (MQ=1)         gGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACC            <  2:744896/100‑1 (MQ=1)         gGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACC            <  2:2289756/100‑1 (MQ=1)         gGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACC            <  1:130646/100‑1 (MQ=1)         gGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACC            >  1:1258730/2‑101 (MQ=1)          GTTTCGATCCCCGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCa           <  1:1390546/101‑2 (MQ=1)          GTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGGGCGACCa           >  2:1387470/1‑100 (MQ=1)          GTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCa           <  2:2308317/101‑2 (MQ=1)           TTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCag          >  2:4923984/1‑99 (MQ=11)              CGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGTGGAGCGACCagcgc       >  1:4358757/1‑96 (MQ=14)              CGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCagcgc       >  1:851139/1‑96 (MQ=14)              CGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCagcgc       >  1:3977772/1‑96 (MQ=14)               GATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCagcgcg      >  2:5018250/1‑95 (MQ=14)                ATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCagcgcgc     >  1:98905/1‑94 (MQ=14)                  CCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCagcgcgcaa   >  2:4026885/1‑92 (MQ=9)                  CCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCagcgcgcaa   >  1:700807/1‑92 (MQ=9)                  CCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCagcgcgcaa   >  1:2044398/1‑92 (MQ=9)                   CACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCCgcgcgcaat  <  2:180511/101‑10 (MQ=2)                                          |||||||||||||||||||||||||||||||||||                                            TCCCATAGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC..............................................................................  <  NC_014034/1397943‑1397903 ............................................................................GTTTCGATCCACGCCCCCGCGGGGGGAGCGACCCAGCAGGATC  <  NC_014034/1434381‑1434339 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG