New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 392462	27 (0.120)	32 (0.140)	5/198	32.7	0.48	intergenic (‑110/+33)	RCAP_rcc00363/trmD	hypothetical protein/tRNA (guanine‑N1)‑methyltransferase
	?	NC_014034	= 2330174	41 (0.180)					intergenic (+149/+163)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

CTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCCGGGGGCGGAG.CCCC....................................................................................................  >  NC_014034/392362‑392462 .....................................................................................................C.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAGCC  <  NC_014034/2330174‑2330076                                                                                                                                                                                                                                                                                          CGGGGGTGCGGGGGCGGAGCCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGC                        >  2:2590454/1‑101 (MQ=32)                                                                               CGGGGGTGCGGGGGCGGAGCCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGC                        >  2:1389899/1‑101 (MQ=32)                                                                                GGGGGTGCGGGGGCGGAGCCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCC                       >  1:2103477/1‑101 (MQ=32)                                                                                GGGGGTGCGGGGGCGGAGCCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCC                       >  1:4026583/1‑101 (MQ=32)                                                                                 GGGGTGCGGGGGCGGAGCCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCG                      >  2:1772347/1‑101 (MQ=32)                                                                                  GGGTGCGGGGGCGGAGCCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGC                     >  1:358669/1‑101 (MQ=32)                                                                                   GGTGCGGGGGCGGAGCCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCC                    >  2:4376869/1‑101 (MQ=32)                                                                                     tgCGGGGGCGGAGCCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCT                  >  2:1272127/3‑101 (MQ=32)                                                                                        GGGGGCGGAGCCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGG               >  2:352069/1‑101 (MQ=32)                                                                                        GGGGGCGGAGCCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGG               >  2:1143206/1‑101 (MQ=32)                                                                                        GGGGGCGGAGCCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGG               >  2:1339429/1‑101 (MQ=32)                                                                                        GGGGGCGGAG.CCCCAGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGG               >  2:2661408/1‑101 (MQ=14)                                                                                         GGGGCGGAGCCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGC              >  1:1887689/1‑101 (MQ=32)                                                                                         GGGGCGGAGCCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGC              >  2:3294478/1‑101 (MQ=32)                                                                                         GGGGCGGAGCCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGACCTTGGC              >  2:3296802/1‑101 (MQ=17)                                                                                          GGGCGGAGCCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCG             >  2:4090765/1‑101 (MQ=32)                                                                                            GCGGAGCCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGA           >  2:3792962/1‑101 (MQ=11)                                                                                            GCGGAGCCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGA           >  2:4403295/1‑101 (MQ=11)                                                                                             gggcccCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAG          <  1:1961494/95‑1 (MQ=1)                                                                                              ggagcCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGG         >  1:73698/6‑101 (MQ=1)                                                                                              ggagcCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGG         >  2:3974262/6‑101 (MQ=1)                                                                                              ggagcCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGGTGCCGCCCTTGGCGGAGG         >  2:4346917/6‑101 (MQ=1)                                                                                                cccCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCC       <  2:1786215/98‑1 (MQ=1)                                                                                                 ccCCCC.GGCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCA      <  2:3824296/99‑1 (MQ=1)                                                                                                  cCCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAA     >  2:3436649/2‑101 (MQ=1)                                                                                                   CCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAG    <  1:3903213/101‑1 (MQ=1)                                                                                                   CCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAG    >  1:2030083/1‑101 (MQ=1)                                                                                                   CCCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAG    >  2:4400030/1‑101 (MQ=1)                                                                                                    CCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAGC   >  2:3271453/1‑101 (MQ=1)                                                                                                    CCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAGC   >  1:601698/1‑101 (MQ=1)                                                                                                    CCC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAGC   <  1:4394266/101‑1 (MQ=1)                                                                                                     CC.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAGCC  >  1:1082643/1‑101 (MQ=1)                                                                                                                                                                                                            CTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCCGGGGGCGGAG.CCCC....................................................................................................  >  NC_014034/392362‑392462 .....................................................................................................C.GCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAGCC  <  NC_014034/2330174‑2330076 Base quality scores:  ATCG  < 3 ≤  ATCG  < 24 ≤  ATCG  < 31 ≤  ATCG  < 34 ≤  ATCG  < 39 ≤  ATCG