New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1397903 =	198 (1.050)	62 (0.330)	12/130	24.9	0.39	intergenic (+207/+1691)	RCAP_rcc01307/RCAP_rcc01309	hypothetical protein/IS66 family transposase
	?	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.

AGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCGCCCGCGGCGTTTGACCTGGTCGCGG..GCAGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGATTGG  >  NC_014034/1434679‑1434877                                                                                                     |                                                                                                     cgTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCTGGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAac                                                                                                      <  2:81486/100‑1 (MQ=2)                                                                      gTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAt                                 <  1:3896527/101‑1 (MQ=11)                                                                       tCGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATg                                >  2:4989176/1‑101 (MQ=31)                                                                       tCGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATg                                >  2:3499567/1‑101 (MQ=31)                                                                         gcgccccccGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGa                              <  1:5604609/98‑1 (MQ=17)                                                                         gCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGa                              <  2:2473616/101‑1 (MQ=32)                                                                          cTCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGaa                             <  1:4989457/101‑1 (MQ=33)                                                                           tCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGaaa                            >  2:5134898/1‑101 (MQ=34)                                                                           tCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGaaa                            <  1:2796111/101‑1 (MQ=34)                                                                           tCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGaaa                            <  1:5150948/101‑1 (MQ=34)                                                                           cccccccGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGaaa                            <  2:3053914/100‑1 (MQ=21)                                                                            ccccccGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGaaaa                           <  1:2972267/101‑1 (MQ=35)                                                                             cccccGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAAc                          >  2:3530141/1‑101 (MQ=37)                                                                              ccccGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAAcc                         >  2:1401849/1‑101 (MQ=38)                                                                              ccccGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAAcc                         <  1:3834943/101‑1 (MQ=38)                                                                              ccccGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCCTGGATCGAAACATGGAAAAcc                         <  1:4265304/101‑1 (MQ=38)                                                                                ccGCGGTGGCGTGGATCTAAACGACTCGCTGAAGGAGGGTGATCTCGGTGGCACCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACcgc                       <  2:47260/101‑1 (MQ=14)                                                                                ccGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGGTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACcgc                       <  1:2821802/101‑1 (MQ=255)                                                                                ccGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACcgc                       >  2:4065739/1‑101 (MQ=40)                                                                                 cgcgGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACcgcg                      <  1:3467319/101‑1 (MQ=40)                                                                                  gcgGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCGCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCgg                     >  2:600083/1‑101 (MQ=255)                                                                                  gcgGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCGCCCTCGGGGGCGTGGATCGAAACATGGAAAACCGCgg                     >  1:4941509/1‑101 (MQ=255)                                                                                  gcgGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCCCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCgg                     <  1:3941055/101‑1 (MQ=255)                                                                                   cgGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGc                    >  2:2748375/1‑101 (MQ=255)                                                                                   cgGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGc                    <  1:815883/101‑1 (MQ=255)                                                                                   cgGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGc                    <  2:2384186/101‑1 (MQ=255)                                                                                   cgGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAAACGAGGc                    >  2:2516667/1‑101 (MQ=255)                                                                                   cgGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGGGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGc                    >  2:3544506/1‑101 (MQ=255)                                                                                    gggggCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCt                   <  2:3747479/101‑1 (MQ=255)                                                                                    gggggCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCt                   <  1:1142254/101‑1 (MQ=255)                                                                                    gggggCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGCCTCTTCCCCCGCGGGGGCGGGGATCGAAACATGGAAAACCGCGGCt                   >  2:5730553/1‑101 (MQ=14)                                                                                     ggggCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCtt                  >  1:2237143/1‑101 (MQ=255)                                                                                      gggCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTc                 <  1:4571221/101‑1 (MQ=255)                                                                                      gggCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTc                 <  2:1854422/101‑1 (MQ=255)                                                                                      gggCGGGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTc                 >  1:4219917/1‑101 (MQ=255)                                                                                       ggCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCa                <  1:5304107/101‑1 (MQ=255)                                                                                        gCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCAc               <  2:2016351/101‑1 (MQ=255)                                                                                         cGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCAcc              <  1:1690805/101‑1 (MQ=255)                                                                                          gTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACcg             <  1:4989260/101‑1 (MQ=255)                                                                                          gTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACcg             <  1:3499784/101‑1 (MQ=255)                                                                                           tGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAATCGCGGCTTCACcgc            >  2:2851716/1‑101 (MQ=255)                                                                                            ggATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACcgcg           <  1:1329435/101‑1 (MQ=255)                                                                                            ggATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACcgcg           >  1:2196731/1‑101 (MQ=255)                                                                                                cGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCggg       >  2:1346415/1‑101 (MQ=255)                                                                                                cGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCggg       <  1:4699752/101‑1 (MQ=255)                                                                                                 gAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGa      <  1:3926256/101‑1 (MQ=255)                                                                                                 gAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGa      >  2:2086483/1‑101 (MQ=255)                                                                                                 gAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGa      >  1:922068/1‑101 (MQ=255)                                                                                                  aaaCGGCGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCGGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGAt     <  1:5730848/101‑1 (MQ=255)                                                                                                  aaaCGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGAt     >  2:5472730/1‑101 (MQ=255)                                                                                                     cgacgCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGATTgg  >  2:5159447/1‑101 (MQ=255)                                                                                                     cgacgCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGATTgg  <  1:976872/101‑1 (MQ=255)                                                                                                     |                                                                                                     AGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCGCCCGCGGCGTTTGACCTGGTCGCGG..GCAGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGATTGG  >  NC_014034/1434679‑1434877 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 25 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG