New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1395633 =	173 (1.100)	48 (0.310)	4/128	21.7	0.28	intergenic (+445/‑486)	RCAP_rcc01306/RCAP_rcc01307	Cas2 family CRISPR‑associated protein/hypothetical protein
	?	NC_014034	= 1434578	76 (0.310)					intergenic (‑357/‑601)	RCAP_rcc01334/RCAP_rcc01335	hypothetical protein/Fis family GAF modulated sigma54 specific transcriptional regulator
Rejected: Position hash score below cutoff.

GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCGCCCGCGGCGTTTGACCTGGTCGCGG..GCAGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGC  >  NC_014034/1434481‑1434678                                                                                                    |                                                                                                         gTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAaca                                                                                                         <  2:3925431/101‑2 (MQ=2)                                                                     gTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAacac                                 >  1:4845198/1‑101 (MQ=11)                                                                     gTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAacac                                 <  2:1404810/101‑1 (MQ=11)                                                                      tCGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACg                                <  1:3747974/101‑1 (MQ=31)                                                                      tCGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACg                                <  1:3399659/101‑1 (MQ=31)                                                                      tCGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACg                                <  2:4783508/101‑1 (MQ=31)                                                                       cGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACgg                               >  2:2476186/1‑101 (MQ=32)                                                                       cGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACgg                               <  1:2958617/101‑1 (MQ=32)                                                                       cGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGGGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACgg                               >  1:145606/1‑101 (MQ=17)                                                                         cTCCCCCCGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGTGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGAt                             <  2:5027991/101‑1 (MQ=18)                                                                         cTCCCCCCGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGAt                             <  2:1442019/101‑1 (MQ=33)                                                                         cTCCCCCCGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGAt                             <  2:2686272/101‑1 (MQ=33)                                                                         cTCCCCCCGCGGGGGCGTGGATCGAAACCCCGCGGCGTCCCGAAGACGGTCATCT.GGTGCCGCTGCGTCGCTCCCCCCGCGGGGGCGTGGATCGAAacacc                                <  1:4276539/101‑2 (MQ=2)                                                                          tCCCCCCGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGAtt                            >  2:1472486/1‑101 (MQ=34)                                                                           ccccccGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTg                           <  2:3689526/101‑1 (MQ=35)                                                                           ccccccGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTg                           <  1:4033082/101‑1 (MQ=35)                                                                           ccccccGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTg                           >  1:2944675/1‑101 (MQ=35)                                                                           ccccccGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTg                           <  1:1419776/101‑1 (MQ=35)                                                                           ccccccGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTg                           >  2:2909108/1‑101 (MQ=35)                                                                           ccccccGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTg                           <  1:3380468/101‑1 (MQ=35)                                                                            cccccGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGc                          <  2:725605/101‑1 (MQ=37)                                                                            cccccGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGc                          <  1:3278510/101‑1 (MQ=37)                                                                            cccccGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGc                          <  2:4443762/101‑1 (MQ=37)                                                                            cccccGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGc                          <  2:4383141/101‑1 (MQ=37)                                                                             ccccGCGGGGTCGGTGATCTAAACGACGCA....CTGAAGGAGGGTGATCTCTGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCa                         <  1:652419/101‑1 (MQ=14)                                                                             ccccGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCa                         <  1:2219912/101‑1 (MQ=38)                                                                              cccGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCAt                        <  2:4400450/101‑1 (MQ=39)                                                                              cccGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCAt                        <  1:2760898/101‑1 (MQ=39)                                                                              cccGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGAGCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCAt                        <  2:511919/101‑1 (MQ=255)                                                                               ccGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATg                       >  1:2071073/1‑101 (MQ=40)                                                                               ccGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATg                       <  1:1378453/101‑1 (MQ=40)                                                                               ccGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATg                       <  1:4124054/101‑1 (MQ=40)                                                                                cgcgGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATgg                      <  1:3604701/101‑1 (MQ=40)                                                                                cgcgGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATgg                      <  2:3720083/101‑1 (MQ=40)                                                                                 gcgGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGgc                     <  1:4696957/101‑1 (MQ=255)                                                                                 gcgGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGgc                     >  1:3366406/1‑101 (MQ=255)                                                                                 gcgGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGgc                     <  1:1170734/101‑1 (MQ=255)                                                                                  cgGGGGCGTGGATCGAAACGACGCG....CTGAAGGGGGGTGATCTCGGTGGCGCCTTGTCGCTCACCCCGCGGGGGCGTGGATCGAAACACGGATTgattgggg                    >  2:1575157/1‑94 (MQ=11)                                                                                  cgGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGgcg                    >  2:1605330/1‑101 (MQ=255)                                                                                  cgGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGgcg                    <  1:3118721/101‑1 (MQ=255)                                                                                    ggggCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGcc                  <  2:2143806/101‑1 (MQ=255)                                                                                    ggggCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCCCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGcc                  <  1:4816845/101‑1 (MQ=255)                                                                                      ggCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGa                <  1:3882362/101‑1 (MQ=255)                                                                                       gCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAg               <  2:2533244/101‑1 (MQ=255)                                                                                       gCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAg               >  1:898219/1‑101 (MQ=255)                                                                                         gTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAggg             <  2:4820585/101‑1 (MQ=255)                                                                                         gTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAggg             >  2:2375973/1‑101 (MQ=255)                                                                                         gTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAggg             >  1:4972542/1‑101 (MQ=255)                                                                                          tGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGa            >  1:2711100/1‑101 (MQ=255)                                                                                          tGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGa            <  2:552114/101‑1 (MQ=255)                                                                                           ggataggcacgccgCG....GTGAAGGCGGGTTATCCCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACAGATTGCATGGCGCCGAGGGAc           <  2:4359400/93‑1 (MQ=17)                                                                                           ggATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGAc           <  1:1491063/101‑1 (MQ=255)                                                                                           ggATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGAc           >  2:5010800/1‑101 (MQ=255)                                                                                           ggATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGAc           <  1:3022801/101‑1 (MQ=255)                                                                                            gATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGTGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACa          <  2:4335822/101‑1 (MQ=255)                                                                                            gATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACa          <  1:2636083/101‑1 (MQ=255)                                                                                             aTCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAg         <  1:2049442/101‑1 (MQ=255)                                                                                             aTCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAg         <  2:3746099/101‑1 (MQ=255)                                                                                             aTCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAg         <  2:4844871/101‑1 (MQ=255)                                                                                               cGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGGATGGGGCCGAGGGACAGGc       >  2:4503355/1‑101 (MQ=255)                                                                                               cGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGc       >  2:4878517/1‑101 (MQ=255)                                                                                                gAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCt      >  2:3900824/1‑101 (MQ=255)                                                                                                 aaaCGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCTAGGGACAGGCtt     <  1:2738057/101‑1 (MQ=255)                                                                                                 aaaCGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCtt     <  1:248210/101‑1 (MQ=255)                                                                                                  aaCGGCGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCttt    <  1:2704365/101‑1 (MQ=255)                                                                                                  aaCGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCttt    <  2:821804/101‑1 (MQ=255)                                                                                                  aaCGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCttt    <  1:242288/101‑1 (MQ=255)                                                                                                  aaCGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCttt    <  2:2887098/101‑1 (MQ=255)                                                                                                  aaCGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCttt    <  1:3083613/101‑1 (MQ=255)                                                                                                  aaCGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCttt    <  2:2152155/101‑1 (MQ=255)                                                                                                   acgacgCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTg   <  2:2472279/101‑1 (MQ=255)                                                                                                   acgacgCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTg   <  2:703303/101‑1 (MQ=255)                                                                                                   acgacgCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTg   <  1:1343573/101‑1 (MQ=255)                                                                                                   acgacgCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTg   <  2:119928/101‑1 (MQ=255)                                                                                                    cgacgCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGc  <  1:2086157/101‑1 (MQ=255)                                                                                                    cgacgCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGc  <  1:3392271/101‑1 (MQ=255)                                                                                                    cgacgCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGc  >  2:5029064/1‑101 (MQ=255)                                                                                                    |                                                                                                         GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCGCCCGCGGCGTTTGACCTGGTCGCGG..GCAGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCG....CTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACACGGATTGCATGGCGCCGAGGGACAGGCTTTGC  >  NC_014034/1434481‑1434678 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 25 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG