New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1397301 =	133 (0.900)	22 (0.150)	7/140	22.1	0.25	coding (1183/1578 nt)	RCAP_rcc01307	hypothetical protein
	?	NC_014034	= 1434780	NA (NA)					intergenic (‑559/‑399)	RCAP_rcc01334/RCAP_rcc01335	hypothetical protein/Fis family GAF modulated sigma54 specific transcriptional regulator
Rejected: Position hash score below cutoff.

GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGATTGGGTC  >  NC_014034/1434746‑1434880                                   |                                                                                                     gTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAt                                    >  2:2507771/1‑101 (MQ=11) gTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAt                                    <  1:2368142/101‑1 (MQ=11) gTCGCCCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACAt                                    <  1:3506982/101‑1 (MQ=11)   cGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATgg                                  >  1:154781/1‑101 (MQ=32)    gCTCCCCCCGGGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGTTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGa                                 <  1:3847700/101‑1 (MQ=12)    gCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGa                                 <  2:2983896/101‑1 (MQ=32)     cTCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGaa                                <  2:3701665/101‑1 (MQ=33)      tCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGaaa                               >  2:1299796/1‑101 (MQ=34)      cccccccGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGaaa                               <  2:2266261/100‑1 (MQ=21)       ccccccGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGaaaa                              <  2:541261/101‑1 (MQ=35)        cccccGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAAc                             <  2:2217794/101‑1 (MQ=37)         ccccGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAAcc                            <  1:2278926/101‑1 (MQ=38)          cccGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCNCGGTGGCGTGGATCGAAACATGGAAAACcg                           >  1:2628246/1‑101 (MQ=255)          cccGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACcg                           <  1:3213961/101‑1 (MQ=39)          cccGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACcg                           >  1:711903/1‑101 (MQ=39)           ccGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACcgc                          >  2:1514911/1‑101 (MQ=40)             gcgGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCgg                        >  1:1800789/1‑101 (MQ=255)             gcgGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCgg                        >  2:2993527/1‑101 (MQ=255)               gggggCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCt                      >  2:3968972/1‑101 (MQ=255)               gggggCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCt                      >  2:3490566/1‑101 (MQ=255)                 gggCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTc                    <  1:4011724/101‑1 (MQ=255)                  ggCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCa                   >  2:126941/1‑101 (MQ=255)                  ggCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCa                   <  2:127077/101‑1 (MQ=255)                   gCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCAc                  <  2:3667103/101‑1 (MQ=255)                    cGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCAcc                 <  2:2315684/101‑1 (MQ=255)                    agTGGAGCGAAACGACGCGCTGAAGGAGGGTGATCGCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCAcc                 <  2:64228/100‑1 (MQ=255)                     gTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACcg                <  1:1485023/101‑1 (MQ=255)                        gATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACcgcgc             >  2:1557659/1‑101 (MQ=255)                        gATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACcgcgc             <  2:4139129/101‑1 (MQ=255)                         aTCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACcgcgcg            <  1:3849135/101‑1 (MQ=255)                          tCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCgg           >  1:3326077/1‑101 (MQ=255)                          tCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCgg           <  1:1304427/101‑1 (MQ=255)                           cGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCggg          <  2:1590809/101‑1 (MQ=255)                           cGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCggg          <  2:1944194/101‑1 (MQ=255)                           cGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCggg          >  2:3925608/1‑101 (MQ=255)                           cGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCATGTCGCTCCGCCCGCGGGGGCGGGTCTCGATACATGGAAAACCCCGGATTCACcgcggtgg          >  2:3477848/1‑97 (MQ=17)                            gAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGa         >  2:2168870/1‑101 (MQ=255)                            gAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGa         >  1:3916295/1‑101 (MQ=255)                            gAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGa         <  1:1316408/101‑1 (MQ=255)                               acgacgCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGATTg      >  1:3151396/1‑101 (MQ=255)                               acgacgCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGATTg      <  1:1634644/101‑1 (MQ=255)                                cgacgCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGATTgg     >  2:661115/1‑101 (MQ=255)                                cgacgCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGATTgg     <  1:424841/101‑1 (MQ=255)                                 gacgCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGATTggg    <  2:3825654/101‑1 (MQ=255)                                 gacgCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGATTggg    >  2:2591796/1‑101 (MQ=255)                                 gacgCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGATTggg    <  1:4110187/101‑1 (MQ=255)                                 gacgCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGATTggg    <  1:2174971/101‑1 (MQ=255)                                  acgCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGATTGGGt   >  2:3153305/1‑101 (MQ=255)                                  acgCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGATTGGGt   <  1:1263338/101‑1 (MQ=255)                                   cgcgCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCTCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGATTGGGTc  <  1:1053879/101‑1 (MQ=255)                                   |                                                                                                     GTCGCTCCCCCCGCGGGGGCGTGGATCGAAACGACGCGCTGAAGGAGGGTGATCTCGGTGGCGCCTTGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACATGGAAAACCGCGGCTTCACCGCGCGGGATTGGGTC  >  NC_014034/1434746‑1434880 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG