New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1732870 =	28 (0.150)	31 (0.170)	12/154	24.2	0.51	intergenic (‑294/‑109)	RCAP_rcc01601/tgt	FeS assembly SUF system protein/queuine tRNA‑ribosyltransferase
	?	NC_014034	= 2474937	32 (0.130)					intergenic (‑100/+26)	RCAP_rcc02301/engA	hypothetical protein/GTP‑binding protein EngA
Rejected: Position hash score below cutoff.

AACAGGCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCC....GT...C....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGGCGCTGCTAAACGCGCGCCAAAGG  >  NC_014034/1732790‑1732970                                                                                               |                                                                                                       aaCAGGCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTGCGGGGGGGCGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGa                                                                                       <  1:3070274/101‑1 (MQ=21)      gCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.Ga                                                                                 <  1:3828337/101‑1 (MQ=21)      gCAAGGCCCCTGTTTTTCCCAGGGAAAATT.CCCCTTTTTTTTTTTGGGGGGGGGGGGGGGGGGCCC..CCCCCC....GG...CGGGTCGCCGCGGGCTTGCCCGAGGC.g                                                                                  <  2:2473163/101‑1 (MQ=2)        aaGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCC....GCGGGT....CGCCTCGGGCTTGCCCGAGGC.Gaaa                                                                               <  2:625536/101‑1 (MQ=18)         agacccctGCTTTTCCTAGGAAAATGC.CGCCCTTTTTTC.TTTCGGGGGGGGCGGGGGTAAAG..CCCCCCCGCGGG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAg                                                                              <  2:2041340/97‑1 (MQ=2)              cccGTTTTTCCCAGGCAAAATG.CGCCCTTCTTTCTTTTGGGGGGGGGGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTcc                                                                         <  1:2131675/101‑1 (MQ=17)              cccGCTTTTCCTAGGCAAAATC.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTcc                                                                         <  1:2819242/101‑1 (MQ=18)                 gCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAC..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTccccc                                                                      <  1:612871/101‑1 (MQ=21)                  cTTTTCCTAGGCAAAATC.CGCCCTGCTTTCTTTGCGGGGGGGCGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTcccccc                                                                     <  2:2216636/101‑1 (MQ=17)                       ccTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGaa                                                                <  2:3038981/101‑1 (MQ=21)                         tAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGaaaa                                                              <  1:4631361/101‑1 (MQ=21)                         tAGCCAAAATC.CGCCTTTTTTTCTTTGGGGGGGGGCGGGGGGTAAAC..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGaaaa                                                              <  1:1388593/101‑1 (MQ=9)                         caagCAAAATCCCGCCTTTTTTTCTTTGGGGGGGGGGGGGGGGTAACC..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGaaa                                                               <  2:4139376/98‑1 (MQ=2)                           ggCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAAcc                                                            <  1:2228877/101‑1 (MQ=21)                            gaaaagTA.CCCCCTTCTTTCTTTCGGGGGGGGCGGGGGGTGAAC..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCt                                                           <  2:2568441/99‑1 (MQ=17)                                aaTA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGGGAAGGCCCCCCCG...GG...G....GGCCTCGGGGTTGGCCGCGGCGGGAGGCTCCCCCCCCTGAAAActcgcc                                                        >  2:3650040/1‑96 (MQ=255)                                 aTA.CGCCCTTCTTTCTTTTGGGGGGGGCGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCt                                                      <  2:4638946/101‑1 (MQ=18)                                  atccGCCTTGCTTTCTTTGGGGGGGGGGGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCt                                                      <  2:4515289/98‑1 (MQ=9)                                   tccGCCTTTTTTTCTTTTGGGGGGGGGGGGGGGTGAGC..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTg                                                     <  1:1265839/99‑1 (MQ=12)                                        ccTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTgcgcgc                                                <  2:2866880/101‑1 (MQ=21)                                          ttctttttTTTGGGGGGGGGGGGGGGTAAAC..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGt                                              <  1:2787169/101‑1 (MQ=18)                                                    tggggggggGGGGGGGGGAAC..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCt                                    <  1:1178798/99‑1 (MQ=18)                                                    gggggggggGGGGGGGTGACG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCt                                    <  1:4502018/99‑1 (MQ=18)                                                     ggggggggGGGGGGGTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCt.t                                  <  1:2841421/100‑1 (MQ=18)                                                      gggggggGGGGGGGGGACG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCt.tt                                 <  1:331732/101‑1 (MQ=18)                                                              ggggggTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGGCTGCGCGCGTCGGTTTCCCT.TTCGCCCCgg                         >  2:1558645/1‑101 (MQ=18)                                                              ggggggTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCCGccccg                         >  1:4429828/1‑99 (MQ=21)                                                              ggggggTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCCTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCgg                         >  1:1171363/1‑101 (MQ=21)                                                              ggggggTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCCTGAAAACCTTGCCTGCGCGCGGCGCTTTCCCT.TTCGGccccg                         >  2:3513571/1‑99 (MQ=18)                                                              ggggggTGAAG..CCCCCCGCG.GG...G....CGCCCCGGGCTTGCCCCCGGG.GGAAACTTCCCCCCGCGAAAAACCTGCCCGCGCGCGCCGCCTTCCCTCTTCGCCCCg                          >  1:3965202/1‑101 (MQ=255)                                                               gggggTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCggg                        >  2:1492929/1‑100 (MQ=21)                                                               gggggTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGgc                        >  2:2282214/1‑101 (MQ=21)                                                               gggggTGAAG..CCCCCCGCG.GG...T....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGgc                        >  2:1473257/1‑101 (MQ=21)                                                                                      ccggcgcgtcGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGGCGCTGCTAAAcgcg           <  2:921582/92‑1 (MQ=255)                                                                                         gcgggtcGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGGCGCTGCTAAACgcgcgc        <  1:4432990/95‑1 (MQ=255)                                                                                         gcgggtcGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGGCGCTGCTAAACgcgcgc        <  2:551788/95‑1 (MQ=255)                                                                                          cgggtcGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGGCGCTGCTAAACGCGCGcc       >  1:781341/6‑101 (MQ=255)                                                                                          cgggtcGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGGCGCTGCTAAACGCGCGcc       >  1:4279851/6‑101 (MQ=255)                                                                                           gggtcGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGGCGCTGCTAAACGCGCGCCa      <  2:191912/97‑1 (MQ=255)                                                                                           gggtcGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGGCGCTGCTAAACGCGCGCCa      <  2:3642540/97‑1 (MQ=255)                                                                                           gggtcGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGGCGCTGCTAAACGCGCGCCa      >  1:3628615/5‑101 (MQ=255)                                                                                            ggtcGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGGCGCTGCTAAACGCGCGCCaa     <  1:3513829/98‑1 (MQ=255)                                                                                            ggtcGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGGCGCTGCTAAACGCGCGCCaa     >  1:1937404/4‑101 (MQ=255)                                                                                               cGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGGCGCTGCTAAACGCGCGCCAAAgg  >  1:936604/1‑101 (MQ=255)                                                                                               cGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGGCGCTGCTAAACGCGCGCCAAAgg  >  1:590915/1‑101 (MQ=255)                                                                                               cGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGGCGCTGCTAAACGCGCGCCAAAgg  >  1:1814819/1‑101 (MQ=255)                                                                                               |                                                                                                       AACAGGCAAGGGCCCCGCTTTTCCTAGGCAAAATA.CGCCCTTCTTTCTTTTCGGGGGGGCGGGGGGTGAAG..CCCCCC....GT...C....CGCCTCGGGCTTGCCCGAGGC.GAAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCT.TTCGGCCCGGCGCTGCTAAACGCGCGCCAAAGG  >  NC_014034/1732790‑1732970 Base quality scores:  ATCG  < 3 ≤  ATCG  < 10 ≤  ATCG  < 21 ≤  ATCG  < 32 ≤  ATCG  < 39 ≤  ATCG