New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1396605	131 (0.950)	33 (0.240)	3/130	24.7	0.34	coding (487/1578 nt)	RCAP_rcc01307	hypothetical protein
	?	NC_014034	1397766 =	0 (0.000)					intergenic (+70/+1828)	RCAP_rcc01307/RCAP_rcc01309	hypothetical protein/IS66 family transposase
Rejected: Position hash score below cutoff.

CCGCGCCAAGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACG.......................................................................................................................................  >  NC_014034/1396564‑1396605 .............................................................................GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCGTGGATCGAA  >  NC_014034/1397766‑1397865                                           |||||||||||||||||||||||||||||||||||                                                                                                     cgggctatcGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGG                                                                              <  1:1363053/92‑1 (MQ=0)   ggctatcGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGAT                                                                            <  1:1265166/94‑1 (MQ=1)   ggctatcGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGAT                                                                            <  2:2943274/94‑1 (MQ=1)    gctatcGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATC                                                                           <  2:3689584/95‑1 (MQ=1)    gctatcGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATC                                                                           <  1:4103861/95‑1 (MQ=1)     ttatcGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCG                                                                          <  2:512343/96‑1 (MQ=1)     ctatcGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCG                                                                          <  2:3909026/96‑1 (MQ=1)      tatcGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGc                                                                         >  1:512400/5‑100 (MQ=1)      tatcGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGA                                                                         >  2:2813122/5‑101 (MQ=1)       atcGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                                                                        >  2:3253669/4‑101 (MQ=1)       atcGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                                                                        >  2:2043874/4‑101 (MQ=1)       atcGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                                                                        >  2:1583620/4‑101 (MQ=1)       atcGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAA                                                                        >  1:3139733/4‑101 (MQ=1)        tcGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA                                                                       >  2:4067721/3‑101 (MQ=1)        tcGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA                                                                       >  1:1696140/3‑101 (MQ=1)         cGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC                                                                      >  2:836257/2‑101 (MQ=1)         cGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC                                                                      >  2:3618542/2‑101 (MQ=1)         cGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAAC                                                                      <  2:292905/100‑1 (MQ=1)          GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACG                                                                     >  2:3377662/1‑101 (MQ=1)            CGCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGct                                                                   <  2:896233/101‑3 (MQ=1)             gcgCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTG                                                                  <  1:648318/98‑1 (MQ=0)             GCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTG                                                                  <  2:639350/101‑1 (MQ=1)             GCTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTG                                                                  >  1:2438902/1‑101 (MQ=1)              CTCCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGc                                                                 >  2:2861610/1‑100 (MQ=1)                CCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGctg                                                               >  2:2927319/1‑98 (MQ=1)                CCCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGctg                                                               <  1:2122348/101‑4 (MQ=1)                 CCCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGctga                                                              >  2:1438207/1‑97 (MQ=0)                  CCCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGctgac                                                             >  1:3279536/1‑96 (MQ=0)                   CCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGctgaca                                                            <  1:3223744/101‑7 (MQ=0)                   CCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGctgaca                                                            <  1:3862991/101‑7 (MQ=0)                   CCCGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGctgaca                                                            >  1:509635/1‑95 (MQ=0)                     CGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGctgacacc                                                          <  2:3801100/101‑9 (MQ=0)                     CGCGGGGGCGTGGATCGAAACGGGTCGAAGACCTGCTTGACGCGCTGGATCTGCGGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGCTGctgacacc                                                          <  2:1064008/101‑9 (MQ=0)                                                                    gggctcgatCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCG           >  1:2031740/10‑101 (MQ=0)                                                                    gggctcgatCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCG           <  1:3230029/92‑1 (MQ=0)                                                                    gggctcgatCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCG           >  2:3429242/10‑101 (MQ=0)                                                                    gggcgcgatCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCG           <  1:1293957/92‑1 (MQ=0)                                                                      gctcgatCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCGTG         >  2:2673782/8‑101 (MQ=0)                                                                       ctcgatCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCGTGG        <  2:3068910/95‑1 (MQ=0)                                                                       ctcgatCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCGTGG        >  1:2390147/7‑101 (MQ=0)                                                                       ctcgatCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCGTGG        <  2:2362293/95‑1 (MQ=0)                                                                        tcgatCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCGTGGA       >  1:1650951/6‑101 (MQ=1)                                                                         cgatCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCGTGGAT      >  2:1497543/5‑101 (MQ=1)                                                                         cgatCGTCGCTCCCCCCGCGGGGGCGGGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCGTGGAT      >  1:4008347/5‑101 (MQ=0)                                                                         ccaGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCGTGGAT      <  2:2503213/98‑1 (MQ=1)                                                                          gatCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCGTGGATC     <  2:1455631/98‑1 (MQ=1)                                                                          gatCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCGTGGATC     >  2:729192/4‑101 (MQ=1)                                                                           atCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCGTGGATCG    <  1:2924127/99‑1 (MQ=1)                                                                           atCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCGTGGATCG    >  2:2462182/3‑101 (MQ=1)                                                                             CGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCGTGGATCGAA  <  2:4008087/101‑1 (MQ=1)                                                                             CGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCGTGGATCGAA  >  1:1652140/1‑101 (MQ=1)                                                                             CGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCGTGGATCGAA  <  2:971388/101‑1 (MQ=1)                                           |||||||||||||||||||||||||||||||||||                                                                                                     CCGCGCCAAGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACG.......................................................................................................................................  >  NC_014034/1396564‑1396605 .............................................................................GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGGTGTCCAGCGTCACATGCAGCGGCGTCGCATCGCCATGTCGCTCCCCCCGCGGGGGCGTGGATCGAA  >  NC_014034/1397766‑1397865 Base quality scores:  ATCG  < 3 ≤  ATCG  < 19 ≤  ATCG  < 26 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG