New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 392462	60 (0.250)	33 (0.140)	2/198	29.6	0.41	intergenic (‑110/+33)	RCAP_rcc00363/trmD	hypothetical protein/tRNA (guanine‑N1)‑methyltransferase
	?	NC_014034	1253896 =	36 (0.150)					intergenic (+54/+37)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
Rejected: Position hash score below cutoff.

CTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCCGGGGGCGGA.G.CCCC....................................................................................................  >  NC_014034/392362‑392462 ......................................................................................................CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTCCGG  >  NC_014034/1253896‑1253995                                                                                                                                                                                                                                                                                           CGGGGGTGCGGGGGCGGA.GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGC                         >  1:1864881/1‑101 (MQ=32)                                                                               CGGGGGTGCGGGGGCGGA.GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGC                         >  1:280850/1‑101 (MQ=32)                                                                                GGGGGTGCGGGGGCGGA.GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCC                        >  1:1693991/1‑101 (MQ=32)                                                                                GGGGGTGCGGGGGCGGA.GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCC                        >  1:385865/1‑101 (MQ=32)                                                                                 GGGGTGCGGGGGCGGA.GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCC                       >  2:4918021/1‑101 (MQ=32)                                                                                 GGGGTGCGGGGGCGGA.GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCC                       >  2:2688040/1‑101 (MQ=32)                                                                                  GGGTGCGGGGGCGGA.GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCG                      >  2:312837/1‑101 (MQ=32)                                                                                   GGTGCGGGGGCGGA.GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGG                     >  1:3069058/1‑101 (MQ=32)                                                                                   GGTGCGGGGGCGGA.GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGG                     >  1:4507298/1‑101 (MQ=32)                                                                                    gtgCGGGGGCGGA.GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGT                    >  1:2638850/4‑101 (MQ=32)                                                                                     tgCGGGGGCGGA.GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTG                   >  2:2696591/3‑101 (MQ=31)                                                                                      ggGGGGGCGGACC.CCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGC                  <  2:3190353/99‑1 (MQ=1)                                                                                      gCGGGGGCGGA.GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTTCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGC                  >  2:2897215/2‑101 (MQ=11)                                                                                        GGGGGCGGA.GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCCGGAAATTCGAGATGATCCGCAGCCCGGTGCGC                >  1:83481/1‑101 (MQ=1)                                                                                        GGGGGCGGA.GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGC                >  2:1808640/1‑101 (MQ=1)                                                                                        GGGGGCGGA.GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGC                >  2:1768042/1‑101 (MQ=1)                                                                                        GGGGGCGGA.GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGC                >  2:4519202/1‑101 (MQ=1)                                                                                         aGGGCGGA.GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGCTGATCCGCAGCCCGGTGCGCT               >  1:50977/2‑101 (MQ=1)                                                                                           cgcgcccccCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTG              <  1:3585577/92‑1 (MQ=0)                                                                                             CGGA.GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGA           >  2:4934030/1‑101 (MQ=1)                                                                                               ggagcCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGAT          >  1:385677/6‑101 (MQ=1)                                                                                               cccccCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGAT          <  2:1251963/96‑1 (MQ=1)                                                                                                gagcCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATT         >  1:2593273/5‑101 (MQ=1)                                                                                                 gccCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTT        <  1:3634218/98‑1 (MQ=1)                                                                                                 cccCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTT        <  1:4834091/98‑1 (MQ=1)                                                                                                 cccCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTT        <  2:4863526/98‑1 (MQ=1)                                                                                                 agcaCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTT        >  2:2105458/5‑101 (MQ=1)                                                                                                 agcCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTT        >  2:188010/4‑101 (MQ=1)                                                                                                 agcCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTT        >  1:1373676/4‑101 (MQ=1)                                                                                                  gcCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTC       >  1:260268/3‑101 (MQ=1)                                                                                                    CCCGGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTC     <  1:62400/101‑1 (MQ=1)                                                                                                     CCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTCC    <  2:2239745/101‑1 (MQ=1)                                                                                                     CCCCCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTCC    <  2:2567642/101‑1 (MQ=1)                                                                                                                                                                                                             CTCCTTGTCACCGCGCAAGACTATGCGGCCCAAACCGGAGGGACAATGGCAGGCCATTTCATCTTGCCTCAAATATCCCGGGGGTCCGGGGGCGGA.G.CCCC....................................................................................................  >  NC_014034/392362‑392462 ......................................................................................................CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTCCGG  >  NC_014034/1253896‑1253995 Base quality scores:  ATCG  < 3 ≤  ATCG  < 17 ≤  ATCG  < 24 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG