New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1397903 =	147 (0.920)	44 (0.280)	2/130	24.0	0.30	intergenic (+207/+1691)	RCAP_rcc01307/RCAP_rcc01309	hypothetical protein/IS66 family transposase
	?	NC_014034	= 1434645	61 (0.250)					intergenic (‑424/‑534)	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 ............................................................................GTTTCGATCCACGCCCCCGCGGGGGGAGCGACAAGGCGCCAC  <  NC_014034/1434645‑1434604                                          |||||||||||||||||||||||||||||||||||                                           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           <  2:3711699/100‑2 (MQ=1)         gGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACc           <  2:744896/100‑2 (MQ=1)         gGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACc           <  2:2289756/100‑2 (MQ=1)         gGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACc           <  1:130646/100‑2 (MQ=1)         gGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACc           >  1:1258730/2‑100 (MQ=1)          GTTTCGATCCCCGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACca          <  1:1390546/101‑3 (MQ=1)          GTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGGGCGACca          >  2:1387470/1‑99 (MQ=1)          GTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACca          <  2:2308317/101‑3 (MQ=1)           TTTCGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCAG         >  2:4923984/1‑101 (MQ=11)              CGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGTGGAGCGACCAGcgc      >  1:4358757/1‑98 (MQ=14)              CGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCAGcgc      >  1:851139/1‑98 (MQ=14)              CGATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCAGcgc      >  1:3977772/1‑98 (MQ=14)               GATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCAGcgcg     >  2:5018250/1‑97 (MQ=14)                ATCCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCAGcgcgc    >  1:98905/1‑96 (MQ=14)                  CCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCAGcgcgcaa  >  2:4026885/1‑94 (MQ=9)                  CCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCAGcgcgcaa  >  1:700807/1‑94 (MQ=9)                  CCACGCCCCCGCGGGGGGAGCGACGATCGAGCCCGGCCGATTGCGGATCTGGTCATCAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCAGcgcgcaa  >  1:2044398/1‑94 (MQ=9)                                          |||||||||||||||||||||||||||||||||||                                           TCCCATAGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC.............................................................................  <  NC_014034/1397943‑1397903 ............................................................................GTTTCGATCCACGCCCCCGCGGGGGGAGCGACAAGGCGCCAC  <  NC_014034/1434645‑1434604 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG