New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1397434 =	177 (1.130)	56 (0.360)	11/132	22.0	0.26	coding (1316/1578 nt)	RCAP_rcc01307	hypothetical protein
	?	NC_014034	= 1397936	144 (0.610)					intergenic (+240/+1658)	RCAP_rcc01307/RCAP_rcc01309	hypothetical protein/IS66 family transposase
Rejected: Position hash score below cutoff.

CGATCCACGCCCCCGCGGGGGGAGCGACCGGTGGTGCAGGGCGGTTGCGTGGTGATGACGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC...............................................................................  <  NC_014034/1397527‑1397434 ................................................................................................................................GAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGTTGGTGAGA  <  NC_014034/1397936‑1397892                                                                                               ||||||||||||||||||||||||||||||||||                                              CGATCCACGCCCCCGCGGGGGGAGCGACCGGTGGTGCAGGGCGGTTGCGTGGTGATGACGGTGTTTCTATCCACGCCCCCGCGGGGGGAGCGACCggtcgc                                                                          >  1:3998045/1‑95 (MQ=0)                                                  tgcggcgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGC                         >  1:999628/11‑101 (MQ=0)                                                  tgcggcgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGC                         >  1:3209574/11‑101 (MQ=0)                                                  tgcggcgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGC                         >  1:1578890/11‑101 (MQ=0)                                                   gcggcgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCG                        >  1:948913/10‑101 (MQ=0)                                                    gggcgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGG                       <  1:2768590/93‑1 (MQ=0)                                                    cggcgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGG                       >  1:3249901/9‑101 (MQ=0)                                                    cggcgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGG                       >  2:1868317/9‑101 (MQ=0)                                                    cggcgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGG                       >  1:1029870/9‑101 (MQ=0)                                                     ggcgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGG                      <  2:1878752/94‑1 (MQ=0)                                                       cgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGG                    >  1:3368537/6‑101 (MQ=1)                                                       cgccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGG                    <  1:1403224/96‑1 (MQ=1)                                                        gccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGG                   >  1:4104686/5‑101 (MQ=1)                                                        gccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGG                   <  1:4333310/97‑1 (MQ=1)                                                        gccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGG                   <  2:3881684/97‑1 (MQ=1)                                                        gccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGG                   <  2:2698902/97‑1 (MQ=1)                                                        gccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGG                   <  2:2781279/97‑1 (MQ=1)                                                         ccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCCCCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGA                  <  2:4592278/98‑1 (MQ=0)                                                         ccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCTATCCACGCCCCCGCGGGGGGA                  <  1:2642608/98‑1 (MQ=0)                                                         ccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGA                  <  2:129795/98‑1 (MQ=1)                                                         ccgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGA                  <  1:732437/98‑1 (MQ=1)                                                          cgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGgg                 >  2:3645967/3‑99 (MQ=1)                                                          cgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGgg                 >  2:3285940/3‑99 (MQ=1)                                                          cgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAG                 <  1:1627564/99‑1 (MQ=1)                                                          cgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAG                 <  2:2501011/99‑1 (MQ=1)                                                          cgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAG                 >  1:4326623/3‑101 (MQ=1)                                                          cgGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAG                 <  1:4012192/99‑1 (MQ=1)                                                           gGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGC                <  1:535910/100‑1 (MQ=1)                                                           gGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGC                <  1:416133/100‑1 (MQ=1)                                                            ggtcgTTCGATCCACGCCCCCGGGGGGGGAGCGACCACCGGCCTGACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCG               <  1:3131705/96‑1 (MQ=0)                                                            GGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGTCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCG               <  1:566111/101‑1 (MQ=1)                                                            GGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCG               <  1:3511552/101‑1 (MQ=1)                                                            GGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCG               <  1:2890673/101‑1 (MQ=1)                                                             GTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGA              >  2:394976/1‑101 (MQ=1)                                                             GTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGA              >  1:3443481/1‑101 (MQ=1)                                                              TGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC             >  2:708896/1‑101 (MQ=1)                                                              TGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC             >  2:1076338/1‑101 (MQ=1)                                                               GTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACT            <  2:2796313/101‑1 (MQ=32)                                                               GTTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGANCNACT            >  1:1314756/1‑101 (MQ=1)                                                                ttcCGATCCACGCCCCCGGGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCTATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTG           <  2:760971/98‑1 (MQ=0)                                                                TTTCGATCCACGCCCCCGCGGGGGGAGCGACCCCCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTG           <  1:1503479/101‑1 (MQ=1)                                                                TTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTG           >  1:2800545/1‑101 (MQ=1)                                                                TTTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTG           <  1:4535998/101‑1 (MQ=1)                                                                 TTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGa          <  1:3856527/101‑2 (MQ=1)                                                                 TTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGa          >  2:439538/1‑100 (MQ=1)                                                                 TTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGa          >  1:1535494/1‑100 (MQ=1)                                                                 TTCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGa          <  1:1929326/101‑2 (MQ=1)                                                                  TCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaa         <  1:2222085/101‑3 (MQ=1)                                                                  TCGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaa         <  1:2635635/101‑3 (MQ=1)                                                                   CGATCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaat        >  1:3400467/1‑98 (MQ=1)                                                                      TCCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaatctt     <  2:4072194/101‑7 (MQ=1)                                                                       CCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaatcttg    >  2:3194019/1‑94 (MQ=1)                                                                       CCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaatcttg    >  1:2860000/1‑94 (MQ=1)                                                                       CCACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaatcttg    >  1:3209641/1‑94 (MQ=1)                                                                        CACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaatcttga   <  2:605887/101‑9 (MQ=1)                                                                         cCGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaatcttgac  <  1:3519410/100‑10 (MQ=1)                                                                         ACGCCCCCGCGGGGGGAGCGACCACCGGCCTTACCCAGATCGGCGATGTCCTTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGaatcttgac  <  1:4369775/101‑10 (MQ=1)                                                                                               ||||||||||||||||||||||||||||||||||                                              CGATCCACGCCCCCGCGGGGGGAGCGACCGGTGGTGCAGGGCGGTTGCGTGGTGATGACGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC...............................................................................  <  NC_014034/1397527‑1397434 ................................................................................................................................GAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGTTGGTGAGA  <  NC_014034/1397936‑1397892 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG