New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1732870 =	21 (0.120)	31 (0.180)	13/154	21.7	0.51	intergenic (‑294/‑109)	RCAP_rcc01601/tgt	FeS assembly SUF system protein/queuine tRNA‑ribosyltransferase
	?	NC_014034	= 2474937	39 (0.170)					intergenic (‑100/+26)	RCAP_rcc02301/engA	hypothetical protein/GTP‑binding protein EngA
Rejected: Position hash score below cutoff.

CAACAGGCAAGGGCCCCGCTTTTCCT.AGGCAAAATACGCCCTTCTTTCTTTT.CGGGGGGGCGGGGGGTGAAG...CCCCCC.....GT...C...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTC.GGCCCGGCGCTGCTAAACGCGCGCCAAAGG  >  NC_014034/1732789‑1732970                                                                                                  |                                                                                                           acgcgggCCAGGGCCCCCTTTTTCCTGAGGCAAAATCCCCCTTTTTTTTTTTG.GGGGGGGGGGGGGGGTGAAC...CCCCCC.....GC...GGGTCG.CCTC.GGGCTTGccc                                                                                           <  2:225427/96‑1 (MQ=2)   aCAGGCAAGGGCCCCGCTTTTCCT.AGGCAAAATCCGCCCTTCTTTCTTTC.CGGGGGGGCGGGGGGTGAAG...CCCCCC.....GCGGGT...CG.CCTC.GGGCTTGCCCG.Ag                                                                                       <  2:3309517/101‑1 (MQ=18)    cAGGCCAGGGCCCCGCTTTTCCT.AGCCAAAATCCTCCCTTCTTTTCTTG.CGGGTGGGCGGGAGGTGAAG...CCCCCCGCG..GG...T...CG.CCTC.GGGCTTGCCCG.Agg                                                                                      <  2:509640/101‑1 (MQ=9)         cgcggCCCCTCTTTTCCA.AGACAAAA.CCCCCCTTTTTTTTTTT.GGGGGGGGGGGGGGGGGCAC...CCCCCCCCGCGGG...T...CG.CCTC.GGGCTTGCCCG.AGGC.G.aa                                                                                <  2:947871/98‑1 (MQ=2)                   ctgttCCT.AGGCAAAATACGCCCTTCTTTCTTTT.CGGGGGGGCGGGGGGTGAAG...CCCCCCGCG..GG...T...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTcccccc                                                                     <  1:2116335/98‑1 (MQ=18)                      ttCCT.AGGCAAAATACGCCCTTCTTTCTTTT.CGGGGGGGCGGGGGGTGAAG...CCCCCCGCG..GG...T...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTg                                                                  <  1:2103321/101‑1 (MQ=21)                         tagaGGAAAAATCCGCCTTTTTTTCTTTG.GGGGGGGGCGGGGGGTGAAC...CCCCCCGCG..GG...T...CG.CCTC.GGGCTTTCCCG.AGGC.G.AAAGCTTCCCCCCGTGaa                                                                <  2:4334514/98‑1 (MQ=2)                         ctttggCAAAATTCCCCTTTTTTTTTTTG.CGGGGGGGGGGGGGGTGACC...CCCCCCGCG..GG...T...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGaa                                                                <  2:3565551/97‑1 (MQ=9)                              gCAAAATACGCCCTTCTTTCTTTT.CGGGGGGGCGGGGGGTGAAG...CCCCCCGCG..GG...T...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCt                                                           <  2:2080889/101‑1 (MQ=21)                                aaaaTACGCCCTTCTTTCTTTT.CGGGGGGGCGGGGGGGGGAGGC.CCCCCCG....GG...G...CG.CCCCGGGGCTGGCCCC.GGGG.G.AAAGATTCCCCCCCGCAAAACCtt                                                          >  2:622029/1‑101 (MQ=255)                                 aaaTACTCCCTTCTTTGTTTT.GGGGGGGGGGGGGGTTTAAC...CCCGCCGCG..GG...T...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGc                                                        <  1:1401343/101‑1 (MQ=12)                                 aaaTACGCCCTTCTTTCTTTT.CGGGGGGGCGGGGGGTGAAG...CCCCCCGCG..GG...T...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGc                                                        <  1:1049144/101‑1 (MQ=21)                                   atccGCCCTTCTTTCTTTT.GGGGGGGGCGGGGGGGGAAG...CCCCCCGCG..GG...T...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCt                                                      <  2:379879/98‑1 (MQ=17)                                     ccccccTTCTTTCTTTT.CGGGGGGGCGGGGGGTGAAG...CCCCCCGCG..GG...T...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTgc                                                    <  2:675348/98‑1 (MQ=18)                                      cccccTTTTTTTTTTTGGGGGGGGGGGGGGGGTGACC...CCCCCCGCG..GG...T...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTgc                                                    <  1:291304/99‑1 (MQ=9)                                      cccccTTTTTTTTTTT.GGGGGGGGGGGGGGGGGAAC...CCCCCCCGCG.GG...T...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTgc                                                    <  2:1057991/99‑1 (MQ=12)                                      cccccTTCTTTCTTTG.CGGGGGGGGGGGGGGTGAAC...CCCCCCGCG..GG...T...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTgcg                                                   <  1:1281378/99‑1 (MQ=18)                                        cctttctttctTTG.GGGGGGGGCGGGGGGTGAAC...CCCCCCGCG..GG...T...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTgcgcg                                                 <  2:2383413/98‑1 (MQ=17)                                           ttctttctTTT.CGGGGGGGCGGGGGGGGGAGGCCCCCCCC.....GG...G...CGCCCCC.GGCCTCGCCCC.GGGG.G.AAGGCTCCCCCCCCGGAAAACCTTCCCtcccccgg                                               >  2:2593836/1‑94 (MQ=255)                                               ttcttgT.CGGGGGGGCGGGGGGTGAAC...CCCCCCGCG..GG...T...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCt                                          <  2:1771566/101‑1 (MQ=18)                                                   ttt.CGGGGGGGCGGGGGGGGAAG...CCCCCCCCG..GG...G...CG.CCCC.GGGCGTGGCCGCGGGG.G.AAACATCCCCCCCCGGAAAACCTT.CCCGCGCGCGGCGCctttc                                      >  2:1344531/1‑99 (MQ=255)                                                         ggggggCGGGGGGTGAAG...CCCCCCGCG..GG...G...CG.CCTC.CGGCTTGCCCG.GGGCGG.AAACTTTCCCCCCGCGAAAACC.TGCCCTCGCGCGGCGGTTTCCCCTTc                                 >  2:2010236/1‑101 (MQ=255)                                                            gggCGGGGGGTGAAG...CCCCCCGCG..GG...T...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTC.GGc                             <  2:2950318/101‑1 (MQ=21)                                                              gCGGGGGGTGAAG...CCCCCCGCG..GG...G...GG.CCCC.GGGCTTGCCCC.GGGC.GCAAAGTTTCCCCCCGGACAAACCTTGCCCCCCCCCGCGCCTTTCCCTTCC.GGcc                            >  1:333941/1‑101 (MQ=2)                                                                ggggggTGAAG...CCCCCCGCG..GG...T...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTC.GGCCCgg                         >  1:2504441/1‑101 (MQ=21)                                                                ggggggTGAAG...CCCCCCGCG..GG...T...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTC.GGCCCgg                         >  2:132787/1‑101 (MQ=21)                                                                ggggggTGAAG...CCCCCCGCG..GG...T...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTC.GGCCCgc                         >  2:3057275/1‑100 (MQ=21)                                                                 gggggTGAAG...CCCCCCGCG..GG...G...CG.CCTC.CTGCTTGCCCG.AGGC.G.ACACCTTCCCCCCTTGAGACTCTTGCGTGCGCGGGTCCCTTTGTCTCTCTGGCCCgg                         >  2:3685466/1‑101 (MQ=0)                                                                                        ccccgcgggtcG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTC.GGCCCGGCGCTGCTAAAcgc            <  2:198001/91‑1 (MQ=255)                                                                                             cgggtcG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTC.GGCCCGGCGCTGCTAAACGCGCGcc       >  2:2646967/6‑101 (MQ=255)                                                                                              gggtcG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTC.GGCCCGGCGCTGCTAAACGCGCGCCa      >  1:1726404/5‑101 (MQ=255)                                                                                               ggtcG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTC.GGCCCGGCGCTGCTAAACGCGCGCCaa     <  1:2420127/98‑1 (MQ=255)                                                                                                gtcG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTC.GGCCCGGCGCTGCTAAACGCGCGCCaaa    <  1:4210321/99‑1 (MQ=255)                                                                                                 tcG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTC.GGCCCGGCGCTGCTAAACGCGCGCCAAAg   <  1:3126213/100‑1 (MQ=255)                                                                                                 tcG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTC.GGCCCGGCGCTGCTAAACGCGCGCCAAAg   <  1:1409582/100‑1 (MQ=255)                                                                                                  cG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTC.GGCCCGGCGCTGCTAAACGCGCGCCAAAgg  <  2:675821/101‑1 (MQ=255)                                                                                                  |                                                                                                           CAACAGGCAAGGGCCCCGCTTTTCCT.AGGCAAAATACGCCCTTCTTTCTTTT.CGGGGGGGCGGGGGGTGAAG...CCCCCC.....GT...C...CG.CCTC.GGGCTTGCCCG.AGGC.G.AAAGCTTCCCCCCGTGAAAACCTTGCCTGCGCGCGTCGCTTTCCCTTTC.GGCCCGGCGCTGCTAAACGCGCGCCAAAGG  >  NC_014034/1732789‑1732970 Base quality scores:  ATCG  < 3 ≤  ATCG  < 10 ≤  ATCG  < 20 ≤  ATCG  < 32 ≤  ATCG  < 39 ≤  ATCG