New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 392474	27 (0.140)	8 (0.040)	7/166	27.6	0.18	intergenic (‑122/+21)	RCAP_rcc00363/trmD	hypothetical protein/tRNA (guanine‑N1)‑methyltransferase
	?	NC_014034	2330313 =	47 (0.210)					intergenic (+288/+24)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

CAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCC..GGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCCGCCATTCGGCGA  >  NC_014034/392377‑392574                                                                                                       |                                                                                                         ggagtctgcgCGGCCAAAGCGGGGGGGACAGTGCCAGCCTATTTCA.CCTACCCTTAAATCC.CCCGGGGGGCG.GGGGGCGGGCCCCCC..GGCGGGTCGCCTCg                                                                                                       <  2:2054715/92‑1 (MQ=255)       ctggCGGCCCAAACCGGGGGGAAAATGGCAGGCCATTTTC.TCTTGCC.CAAAAATCCCCGGGGGGCCGGGGGGGGGACCCCCC..GGCGGGTCGCCTCGGCGCa                                                                                                  <  2:534198/98‑1 (MQ=16)        tggagccaaaaaCCGGGGGGACACGGGCCGGCTATTTCG.TCTTCCCTCAAAAGC.CCGGGGGGCCC.GGGGGCGCCCCCCCC..GGCGGGTCGCCTCGGCGCAGc                                                                                                <  1:1321046/92‑1 (MQ=12)                ccaaCCGGGGGGGCAACGTGCGGCCCTTTTATTCTTGCCTAAAATGC.CCGGGGGGTCG.GGGGGGAGGCCCCCC..GGCGGGTCGCCTCGGCGCAGCCG.AGGCg                                                                                        <  2:2945227/99‑1 (MQ=9)                                               atcgtccccaaaaTAC.CCGGGGGGCCG.GGGGGCGGGCCCCCC..GGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATcc                                                      <  2:2169086/91‑1 (MQ=21)                                                   tGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCC..GGCGGGGGGCCCCCGCGCCGGCC.GCGCGGAAACACCTGTCG.AACCTCC.CCCCC.ACAACCCgcc                                                  >  2:2886642/1‑101 (MQ=2)                                                   tGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCC..GGCGGGGCGGCCCCGCGCCGCCGCGGGGGAAAACCCTTCCCGCAACTTCC.CCCCC.aacccagc                                                    >  2:2883971/1‑95 (MQ=2)                                                            aaaccccGGGGGGCC.GGGGGGGGGGCCCCCCGGGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGt                                            <  2:633986/97‑1 (MQ=25)                                                             at.CCCGGGGGTCC.GGGGGCGGAGCCCCC..GGCGGGGTGGCCCGGCGCCGCCG.CGGGGGAAAAACCTCACG.AAACTCT.CCCACAAAAACCGCccgccgccccc                                         >  2:1290965/1‑96 (MQ=2)                                                              t.CCCGGGGGTCC.GGGGGCGGAGCCCCC..GGCGGGGGGCCCCGGGGCGGCCC.CGGGGGAAACAAATGCCG.AAATTCTCCCCCC.AAACCCGCCCCCCGGCcccc                                        >  1:224692/1‑100 (MQ=2)                                                              accccGGGGGGCG.GGGGGGGGGGCCCCCCGGGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTcc                                          <  2:3204613/99‑1 (MQ=25)                                                                 gggggggGCG.GGGGGGGGCCCCCCGG.GGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCcgcg                                      <  1:705137/99‑1 (MQ=25)                                                                    ggggTCC.GGGGGCGGAGCCCCC..GGCGGGGGGCCTCCGCGCAGGCC.CGCGGGAAACACTTGCCC.CACCCCT.CCCCC.AAAACCCGCCCCCCGGCCcgccccca                                  >  2:3856438/1‑96 (MQ=9)                                                                             gggggggccccccc..GGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGc                          <  2:3579922/92‑1 (MQ=255)                                                                             ggggCGGAGCCCCC..GGCGGGGCGCCTCCGCGCCGCCC.CGGCGGAAACACATCCCC.CACTTCT.TCCCC.CAACACCCCCCCCGGCCCCGCGCCCAAACTTCGc                          >  2:2568836/1‑101 (MQ=255)                                                                               gggggccccccg..GGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGctc                        <  1:2128352/94‑1 (MQ=255)                                                                                 cGGAGCCCCC..GGCGGGGCGCCCCGGCGCCGCCC.GGGCGGAAACACTTTCCG.AACTTCT.CCCCC.AAATCCCCCCCCCCGGCCCCCGCCCCAGCTTCGccctc                      >  2:4445110/1‑100 (MQ=255)                                                                                      ccccg..GGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTc                 <  2:2749518/101‑1 (MQ=255)                                                                                       cccc..GGCGGGCCCCCTCGGCGCAGCCG.AGGCGATATCTCTTGCCG.AACTTCC.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTcg                <  1:3814161/101‑1 (MQ=38)                                                                                         gccgggcggGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTcg                <  1:4402449/97‑1 (MQ=255)                                                                                              gcggGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCgccgcc           <  1:4136366/101‑1 (MQ=255)                                                                                               cggGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCCGCCa          >  2:79472/1‑101 (MQ=255)                                                                                                gggTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCCGCCAt         >  1:3637505/1‑101 (MQ=255)                                                                                                 ggTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCCGCCAtt        >  2:3696878/1‑101 (MQ=255)                                                                                                   tccccTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCCGCCATTCg      <  2:191984/98‑1 (MQ=255)                                                                                                    cGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCCGCCCTTCgg     >  2:790085/1‑101 (MQ=255)                                                                                                    cGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCCGCCATTCgg     <  1:523437/101‑1 (MQ=255)                                                                                                    cGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCCGCCATTCgg     >  2:814937/1‑101 (MQ=255)                                                                                                     gCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCCGCCATTCGGc    >  1:2121357/1‑101 (MQ=255)                                                                                                       cTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCCGCCATTCGGCGa  >  1:2810835/1‑101 (MQ=255)                                                                                                       cTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCCGCCATTCGGCGa  >  2:3930469/1‑101 (MQ=255)                                                                                                       |                                                                                                         CAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCA.TCTTGCCTCAAATAT.CCCGGGGGTCC.GGGGGCGGAGCCCCC..GGCGGGTCGCCTCGGCGCAGCCG.AGGCGAAATCACTTGCCG.AACTTCT.CCCAC.AAATCCGGCCGCCGGTCCCGCGTCAAAGCTTCGCTCTGCGCTCGCCGCCATTCGGCGA  >  NC_014034/392377‑392574 Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 24 ≤  ATCG  < 32 ≤  ATCG  < 39 ≤  ATCG