New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 2330175	46 (0.190)	28 (0.120)	2/198	29.6	0.36	intergenic (+150/+162)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
	?	NC_014034	= 2995639	53 (0.220)					intergenic (+179/+41)	RCAP_rcc02802/RCAP_rcc02803	membrane dipeptidase/hypothetical protein
Rejected: Position hash score below cutoff.

CCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAA  >  NC_014034/2995539‑2995739                                                                                                      |                                                                                                        ccAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGccc                                                                                                         <  2:4955311/101‑1 (MQ=255)  cAAGGAAACCCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGcccc                                                                                                        <  2:2852373/101‑1 (MQ=255)    aGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGcccccc                                                                                                      <  2:4171502/101‑1 (MQ=255)    aGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGGGCGGGGGGCGGAGcccccc                                                                                                      >  1:2179185/1‑101 (MQ=255)     ggaaccccccTTCGTTCGCCCCCCCCCACCCGGCCGGCGCCCCGCCCCCTTGCTTTCCCTTGGAAAAAACCG.CCGGGGGGTGCGGGGGGCGGAGCCCCCcg                                                                                                     <  2:4396749/95‑1 (MQ=2)     ggAAACCCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCcg                                                                                                     <  2:3747044/101‑1 (MQ=255)     ggAAACCCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCcg                                                                                                     <  2:3696688/101‑1 (MQ=255)     ggAAACCCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCcg                                                                                                     <  2:4748342/101‑1 (MQ=255)      gAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCcg.c                                                                                                   >  1:938565/1‑101 (MQ=255)      gAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGGGCGGGGGGCGGAGCCCCCcg.c                                                                                                   >  2:2321053/1‑101 (MQ=255)         aaCCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.Cggg                                                                                                >  1:438149/1‑101 (MQ=255)           ccccTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTc                                                                                              >  2:512201/1‑101 (MQ=255)                  ggTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCgg                                                                                       >  2:3596453/1‑101 (MQ=255)                     ctcccccccGCCCCCCGCGGGCGGCCCGGCGCCCTACTTTTCGTTGGCAAAAGACG.CGGGGGGGTGGGGGGGGCGGGGCCCCCCG.CGGGTCGCCCCGGCtt                                                                                    <  2:1492511/96‑1 (MQ=12)                      gccgccCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..g                                                                                 >  1:3012808/1‑101 (MQ=255)                         gccCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCg                                                                              >  1:4281372/1‑101 (MQ=255)                            ccGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCgggg                                                                           >  2:1925378/1‑101 (MQ=255)                                     gTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATccc                                                                  >  2:1136024/1‑101 (MQ=255)                                        ggcggcCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GGCGGGGCGAAATcccccc                                                               >  1:4562026/1‑100 (MQ=255)                                                aGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGGAATCCCCCGCTCAGTcc                                                       >  2:4812889/1‑101 (MQ=255)                                                     tttgtttttCCTTGGAAAAATACGCCCGGGGGGTGCGGGGGGCGGAGCCCCCCGCCGGGTCGCCTCGGCGTCAGCCGAGGCGAAATACCCC.CTCAGCcctt                                                     >  1:4542661/6‑99 (MQ=0)                                                           tttCCTTGGAAAAATACGCCCGGGGGGTGCGGGGGGCGGAGCCCCCCGCCGGGTCGCCTCGGCGTCAGCCGAGGCGAAATACCCC.CTCAGCccttcatctt                                               >  1:3168513/1‑93 (MQ=0)                                                           tttCCTGAGAAAAGTCCG.CGGGGGGGGGGGGGGGGCGGGCCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTc                                            <  2:418764/101‑1 (MQ=25)                                                              ccTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGAc                                         >  1:3733821/1‑101 (MQ=255)                                                               cTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGAcc                                        >  2:3085955/1‑101 (MQ=255)                                                                 tGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGGCCCAGAGACTTTCGACCTc                                      >  2:2955337/1‑101 (MQ=255)                                                                  ggCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGCCTTTCGACCTCg                                     >  2:2335625/1‑101 (MQ=255)                                                                   gCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGa                                    >  2:155669/1‑101 (MQ=255)                                                                      aaaatgggggggggggGGGGGGGGGGGGCCCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAAc                                  <  1:1704361/91‑1 (MQ=37)                                                                           cG.CGGGGGGGTGGGGGGGGGGGCCCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTc                            <  2:2882329/101‑1 (MQ=38)                                                                           cG.CCGGGGGGTGGGGGGGGCGGCGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTc                            <  2:5048236/101‑1 (MQ=255)                                                                            ggcgggggggCGGGGGGGGCGCGCCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTc                            <  2:1273000/97‑1 (MQ=38)                                                                            g.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGCACCGGGTCa                           >  1:4945823/1‑101 (MQ=255)                                                                               cGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGCAATCCCCCGCTCAGCCCCCGAGGCTTTCGGCCTCGAACCGGGTCatc                         >  2:4415283/1‑99 (MQ=37)                                                                                ggggggTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGAc                        >  2:3887071/1‑101 (MQ=255)                                                                                ggggggTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGAc                        >  1:4751490/1‑101 (MQ=255)                                                                                 gggggTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..TCCGGGGCGAAATCCCCCCCTCATTGCCAGAGACCTTCGGCCTCGGACCGGGGGAGAcc                       >  1:1571164/1‑100 (MQ=21)                                                                                 gggggTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGGCAGAcg                       >  2:1102215/1‑101 (MQ=255)                                                                                  ggggTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGAcgc                      >  1:1518776/1‑101 (MQ=255)                                                                                    ggTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCgg                    >  2:2036991/1‑101 (MQ=255)                                                                                       gCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATg                 >  1:4392879/1‑101 (MQ=255)                                                                                       gCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATg                 >  1:290871/1‑101 (MQ=255)                                                                                        gggggggGGGGCCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATgc                <  1:3837172/100‑1 (MQ=255)                                                                                        cGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATgc                >  2:1142012/1‑101 (MQ=255)                                                                                         ggggggCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATgcg               >  1:205053/1‑101 (MQ=255)                                                                                           ggggCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGGCAGACGCGGATGCGCa             >  1:911110/1‑101 (MQ=255)                                                                                            gggCGGCCCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGAGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAg            <  1:1051873/101‑1 (MQ=255)                                                                                             ggCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAgg           >  1:2671468/1‑101 (MQ=255)                                                                                             ggCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAgg           >  1:2482425/1‑101 (MQ=255)                                                                                                ggAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCgg        >  2:4049054/1‑101 (MQ=255)                                                                                                  aGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGc      >  1:4627497/1‑101 (MQ=255)                                                                                                  aGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGc      >  1:4248138/1‑101 (MQ=255)                                                                                                    ccccccG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCg    >  2:610852/1‑101 (MQ=255)                                                                                                    ccccccG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCACGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCg    <  2:1571034/101‑1 (MQ=255)                                                                                                      ccccG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGaa  >  2:3937051/1‑101 (MQ=255)                                                                                                      |                                                                                                        CCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCTCGAACCGGGTCAGACGCGGATGCGCAGGCGGGCCGAA  >  NC_014034/2995539‑2995739 Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 22 ≤  ATCG  < 31 ≤  ATCG  < 39 ≤  ATCG