New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1396969 =	174 (1.130)	49 (0.320)	3/130	29.1	0.36	coding (851/1578 nt)	RCAP_rcc01307	hypothetical protein
	?	NC_014034	= 1434777	NA (NA)					intergenic (‑556/‑402)	RCAP_rcc01334/RCAP_rcc01335	hypothetical protein/Fis family GAF modulated sigma54 specific transcriptional regulator
Rejected: Position hash score below cutoff.

ACGACGAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC.......................................................................................................................................  <  NC_014034/1397013‑1396969 ................................................................................GTTTCGATCCACGCCCCCGCGGGGGGAGCGACCAGCTGCCCGCGACCAGGTCAAACGCCGCGGGCGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTG  <  NC_014034/1434777‑1434678                                              |||||||||||||||||||||||||||||||||||                                                                                                     tttgatcatcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCG                                                                                 >  1:4333768/11‑101 (MQ=0) tttgatcatcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCG                                                                                 <  1:4095430/91‑1 (MQ=0)  ttgatcatcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGG                                                                                >  1:558822/10‑101 (MQ=0)  ttgatcatcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGG                                                                                >  1:3283737/10‑101 (MQ=0)   tgatcatcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGG                                                                               >  2:4324849/9‑101 (MQ=0)   tgatcatcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGG                                                                               >  1:3424577/9‑101 (MQ=0)   tgatcatcGATGTTTCGAGCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGG                                                                               <  2:521830/93‑1 (MQ=0)    gatcatcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGG                                                                              >  2:2188897/8‑101 (MQ=0)    gatcatcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGG                                                                              <  1:1722554/94‑1 (MQ=0)    gatcatcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGG                                                                              >  1:2553121/8‑101 (MQ=0)    gatcatcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGG                                                                              >  1:2628110/8‑101 (MQ=0)    gatcatcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGG                                                                              <  1:2610532/94‑1 (MQ=0)     atcatcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGG                                                                             >  1:989310/7‑101 (MQ=1)      tcatcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGG                                                                            <  1:4088146/96‑1 (MQ=1)       catctATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGA                                                                           <  2:1847543/96‑1 (MQ=1)       catcGATGTTTCGATCCACGCCCCCGCGGTGGGAGCGACGCGGTATCGGTGTGCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGA                                                                           <  1:3831201/97‑1 (MQ=0)       catcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGg                                                                           >  2:529006/5‑100 (MQ=1)       catcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGg                                                                           >  1:1947330/5‑100 (MQ=1)       catcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGA                                                                           <  2:1088950/97‑1 (MQ=1)       catcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGA                                                                           <  2:3078909/97‑1 (MQ=1)       catcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGA                                                                           <  1:410738/97‑1 (MQ=1)       catcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGGGTTTCGATCCACGCCCCCGCGGGGGGg                                                                           >  1:2765150/5‑100 (MQ=0)        atcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAG                                                                          <  1:202806/98‑1 (MQ=1)        atcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAG                                                                          <  2:279151/98‑1 (MQ=1)         tcGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGC                                                                         <  2:2015063/99‑1 (MQ=1)          cGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCG                                                                        >  2:1231429/2‑101 (MQ=1)          cGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCG                                                                        >  1:1673210/2‑101 (MQ=1)          cGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCG                                                                        >  2:4330274/2‑101 (MQ=1)          cGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCG                                                                        >  1:2927772/2‑101 (MQ=1)          cGATGTGTCGATCCCCGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCG                                                                        <  2:2297310/100‑1 (MQ=0)           GATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGA                                                                       >  1:3926598/1‑101 (MQ=1)            ATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGCGCGAC                                                                      >  1:4581766/1‑101 (MQ=1)            ATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC                                                                      >  1:3312653/1‑101 (MQ=1)             TGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACg                                                                     >  2:2771772/1‑100 (MQ=1)              GTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgc                                                                    >  2:1202685/1‑99 (MQ=1)              GTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGAGGTCTTTCGATCCACGCCCCCGCGGGGGGAGCGACgc                                                                    >  1:3991238/1‑99 (MQ=0)               TTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgca                                                                   <  2:3025890/101‑4 (MQ=1)               TTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgca                                                                   <  2:2043302/101‑4 (MQ=1)               TTTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgca                                                                   >  2:2065067/1‑98 (MQ=1)                TTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcag                                                                  >  2:1510206/1‑97 (MQ=1)                TTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcag                                                                  >  1:4626361/1‑97 (MQ=1)                TTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcag                                                                  >  1:4388192/1‑97 (MQ=1)                TTCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcag                                                                  <  1:4180787/101‑5 (MQ=1)                 TCGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcagc                                                                 <  2:573027/101‑6 (MQ=1)                  CGATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcagcg                                                                >  1:1588754/1‑95 (MQ=1)                   GATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcagcgg                                                               >  1:362189/1‑94 (MQ=1)                   GATCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcagcgg                                                               >  1:2866016/1‑94 (MQ=1)                     TCCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcagcggca                                                             <  1:901269/101‑10 (MQ=1)                      CCACGCCCCCGCGGGGGGAGCGACGCGGTATCGGTGTTCGCCGCCGACAGGTTCGGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcagcggcac                                                            >  2:370638/1‑91 (MQ=1)                                                                                TGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCAGCTGCCCGCGACCAGGTCAAACGCCGCGGGCGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTG  <  2:3575708/101‑1 (MQ=1)                                              |||||||||||||||||||||||||||||||||||                                                                                                     ACGACGAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC.......................................................................................................................................  <  NC_014034/1397013‑1396969 ................................................................................GTTTCGATCCACGCCCCCGCGGGGGGAGCGACCAGCTGCCCGCGACCAGGTCAAACGCCGCGGGCGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTG  <  NC_014034/1434777‑1434678 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 24 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG