New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1397766 =	1 (0.010)	37 (0.260)	7/134	21.4	0.36	intergenic (+70/+1828)	RCAP_rcc01307/RCAP_rcc01309	hypothetical protein/IS66 family transposase
	?	NC_014034	= 1434846	133 (0.630)					intergenic (‑625/‑333)	RCAP_rcc01334/RCAP_rcc01335	hypothetical protein/Fis family GAF modulated sigma54 specific transcriptional regulator
Rejected: Position hash score below cutoff.

TTCGATCCACGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC.............................................................................  <  NC_014034/1397865‑1397766 .....................................................................................................................................ATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAAGGCGCCAC  <  NC_014034/1434846‑1434803                                                                                                     |||||||||||||||||||||||||||||||||                                             TTCGATCCACGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACG                                                                              >  2:971388/1‑101 (MQ=1) TTCGATCCACGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACG                                                                              >  2:4008087/1‑101 (MQ=1) TTCGATCCACGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACG                                                                              <  1:1652140/101‑1 (MQ=1)   CGATCCACGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGat                                                                            >  1:2924127/1‑99 (MQ=1)   CGATCCACGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGat                                                                            <  2:2462182/101‑3 (MQ=1)    GATCCACGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGatc                                                                           <  2:729192/101‑4 (MQ=1)    GATCCACGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGatc                                                                           >  2:1455631/1‑98 (MQ=1)     ATCCACGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCCCGCCCCCGCGGGGGGAGCGACGatcg                                                                          <  1:4008347/101‑5 (MQ=0)     ATCCACGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGctgg                                                                          >  2:2503213/1‑97 (MQ=1)     ATCCACGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGatcg                                                                          <  2:1497543/101‑5 (MQ=1)      TCCACGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGatcga                                                                         <  1:1650951/101‑6 (MQ=1)       CCACGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGatcgag                                                                        >  2:3068910/1‑95 (MQ=0)       CCACGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGatcgag                                                                        <  1:2390147/101‑7 (MQ=0)       CCACGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGatcgag                                                                        >  2:2362293/1‑95 (MQ=0)        CACGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGatcgagc                                                                       <  2:2673782/101‑8 (MQ=0)          CGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGatcgcgccc                                                                     >  1:1293957/1‑92 (MQ=0)          CGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGatcgagccc                                                                     <  1:2031740/101‑10 (MQ=0)          CGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGatcgagccc                                                                     <  2:3429242/101‑10 (MQ=0)          CGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGatcgagccc                                                                     >  1:3230029/1‑92 (MQ=0)                                                         gagatctacgCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGG                      >  2:283252/11‑101 (MQ=255)                                                         gagatctacgCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGG                      >  2:1202502/11‑101 (MQ=255)                                                          cgatctacgCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGG                     <  1:3109828/92‑1 (MQ=9)                                                          agatctacgCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGG                     >  1:2307054/10‑101 (MQ=9)                                                           gatctacgCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGG                    <  1:2367063/93‑1 (MQ=9)                                                           gatctacgCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGG                    <  2:1583913/93‑1 (MQ=9)                                                            atctacgCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGGGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGG                   >  1:2945279/8‑101 (MQ=255)                                                            atctacgCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGG                   >  1:3683906/8‑101 (MQ=9)                                                            atctacgCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGG                   <  2:953493/94‑1 (MQ=9)                                                             tctacgCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGG                  >  1:3804552/7‑101 (MQ=9)                                                             tctacgCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGG                  <  1:2193943/95‑1 (MQ=9)                                                               tacgCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAG                <  2:4025181/97‑1 (MQ=14)                                                               tacgCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAG                <  2:1805460/97‑1 (MQ=14)                                                               tacgCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGGCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGgg                >  1:3622218/5‑99 (MQ=9)                                                                acgCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGagatcg               >  2:3109597/4‑95 (MQ=9)                                                                acgCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGC               <  2:554750/98‑1 (MQ=14)                                                                acgCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGC               <  1:1424694/98‑1 (MQ=14)                                                                acgCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGAGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGC               >  2:2527389/4‑101 (MQ=9)                                                                   CCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC            <  2:521881/101‑1 (MQ=31)                                                                    CGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACc           >  1:1337728/1‑100 (MQ=11)                                                                    CGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACc           <  2:2272359/101‑2 (MQ=11)                                                                     GTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcg          >  2:1289406/1‑99 (MQ=1)                                                                     GTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcg          >  1:1394292/1‑99 (MQ=1)                                                                     GTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcg          >  2:3104666/1‑99 (MQ=1)                                                                      TTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGGGACcgg         >  1:457378/1‑98 (MQ=0)                                                                      TTTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcgg         >  2:1112195/1‑98 (MQ=1)                                                                       TTCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggc        <  2:900211/101‑5 (MQ=1)                                                                        TCGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggcg       >  1:1280086/1‑96 (MQ=1)                                                                         CGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTGGATCCACGCCCCCGCGGGGGGAGCGACcggcgg      >  1:4208987/1‑95 (MQ=0)                                                                         CGATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggcgg      <  1:2921276/101‑7 (MQ=0)                                                                          GATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggcggg     >  1:2422780/1‑94 (MQ=0)                                                                          GATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggcggg     <  1:247355/101‑8 (MQ=0)                                                                          GATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggcggg     >  1:448258/1‑94 (MQ=0)                                                                           ATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggcggga    >  2:3518092/1‑93 (MQ=0)                                                                           ATCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggcacgc    <  2:1424000/101‑9 (MQ=0)                                                                            TCCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggcgggat   >  1:2586171/1‑92 (MQ=0)                                                                             CCACGCCCCCGCGGGGGGAGCGACGGCGATGTGACCAGCTTCGATGCGGTCAAGCTGATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcggcgggatc  >  2:2729424/1‑91 (MQ=0)                                                                                                     |||||||||||||||||||||||||||||||||                                             TTCGATCCACGCCCCCGCGGGGGGAGCGACATGGCGATGCGACGCCGCTGCATGTGACGCTGGACACCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC.............................................................................  <  NC_014034/1397865‑1397766 .....................................................................................................................................ATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAAGGCGCCAC  <  NC_014034/1434846‑1434803 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG