New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1395899 =	163 (1.090)	44 (0.290)	6/132	24.4	0.35	intergenic (+711/‑220)	RCAP_rcc01306/RCAP_rcc01307	Cas2 family CRISPR‑associated protein/hypothetical protein
	?	NC_014034	= 1434845	NA (NA)					intergenic (‑624/‑334)	RCAP_rcc01334/RCAP_rcc01335	hypothetical protein/Fis family GAF modulated sigma54 specific transcriptional regulator
Rejected: Position hash score below cutoff.

CATGAACGCATCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC......................................................................................................................................  <  NC_014034/1395942‑1395899 ..............................................................................TGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAAGGCGCCACCGAGATCACCCTCCTTCAGCGCGTCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC  <  NC_014034/1434845‑1434746                                             ||||||||||||||||||||||||||||||||||                                                                                                     cgagccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGG                                                                               >  1:1700511/8‑101 (MQ=0)  gagccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGG                                                                              <  1:1615468/95‑1 (MQ=0)  gagccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGG                                                                              <  2:542077/95‑1 (MQ=0)   agccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGG                                                                             <  1:307041/96‑1 (MQ=0)   agccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGG                                                                             >  1:2672591/6‑101 (MQ=0)    gccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGG                                                                            <  2:2200738/97‑1 (MQ=0)     ccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGG                                                                           >  1:954931/4‑101 (MQ=0)     ccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGG                                                                           >  1:143049/4‑101 (MQ=0)      caGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGA                                                                          >  2:1273044/3‑101 (MQ=1)      caGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGA                                                                          <  2:353153/99‑1 (MQ=1)      caGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGA                                                                          >  2:386437/3‑101 (MQ=1)      caGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGA                                                                          <  2:415182/99‑1 (MQ=1)      caGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGA                                                                          <  2:617795/99‑1 (MQ=1)      caGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGGGTTTCGATCCACGCCCCCGCGGGGGGg                                                                          >  1:3237698/3‑100 (MQ=0)       aGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGcg                                                                         >  2:1316548/2‑99 (MQ=0)       aGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAG                                                                         >  1:3095245/2‑101 (MQ=1)       aGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAG                                                                         >  1:1370187/2‑101 (MQ=1)        GCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGC                                                                        >  1:4034304/1‑101 (MQ=1)        GCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGCTGTTTCGATCCACGCCCCCGCGGGGGGAGC                                                                        >  1:308799/1‑101 (MQ=0)         CATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCG                                                                       >  2:3549457/1‑101 (MQ=1)         CATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCG                                                                       >  2:3336388/1‑101 (MQ=1)          atttTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCGGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGA                                                                      <  2:883853/97‑1 (MQ=0)          ataGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGA                                                                      >  2:486905/4‑101 (MQ=1)          ataGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGA                                                                      >  2:2611957/4‑101 (MQ=1)           taGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC                                                                     >  2:3646860/3‑101 (MQ=1)            aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGGACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGGGCGACc                                                                    >  2:2891007/2‑100 (MQ=0)            aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACc                                                                    >  1:1300839/2‑100 (MQ=1)            aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACc                                                                    >  2:4064549/2‑100 (MQ=1)            aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACc                                                                    >  2:1484473/2‑100 (MQ=1)              TTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCGCGCCCCCGCGGGGGGGGCGACcac                                                                  >  1:3480137/1‑98 (MQ=0)               TTCGATCCCCGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcacc                                                                 <  2:4089049/101‑5 (MQ=1)               TTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcacc                                                                 <  1:3928751/101‑5 (MQ=1)               TTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcacc                                                                 <  2:2115785/101‑5 (MQ=1)               TTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcacc                                                                 <  1:2108022/101‑5 (MQ=1)               TTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcacc                                                                 >  1:3439544/1‑97 (MQ=1)                TCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGCGCGACcaccg                                                                >  1:2742676/1‑96 (MQ=1)                TCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccg                                                                <  2:2618932/101‑6 (MQ=1)                TCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccg                                                                >  1:916137/1‑96 (MQ=1)                  GATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccggc                                                              >  1:2849624/1‑94 (MQ=1)                   ATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccggcc                                                             >  1:1704250/1‑93 (MQ=1)                    TCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccggcct                                                            >  1:2635088/1‑92 (MQ=0)                    TCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccggcct                                                            <  2:4069680/101‑10 (MQ=0)                     CCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccggcctt                                                           <  1:486957/101‑11 (MQ=0)                     CCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccggcctt                                                           <  1:1571544/101‑11 (MQ=0)                                                                              GTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAAGGCGCCACCGAGATCACCCTCCTTCAGCGCGTCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC  >  2:3327943/1‑101 (MQ=1)                                             ||||||||||||||||||||||||||||||||||                                                                                                     CATGAACGCATCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC......................................................................................................................................  <  NC_014034/1395942‑1395899 ..............................................................................TGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAAGGCGCCACCGAGATCACCCTCCTTCAGCGCGTCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC  <  NC_014034/1434845‑1434746 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 24 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG