New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1103359 =	90 (0.380)	40 (0.170)	5/200	35.3	0.40	intergenic (‑359/+59)	ugpB/regA2	sn‑glycerol‑3‑phosphate‑binding periplasmic protein ugpB/photosynthetic apparatus regulatory protein RegA
	?	NC_014034	= 2330175	29 (0.120)					intergenic (+150/+162)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

TTTTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCGGAGCCCCC...................................................................................................  <  NC_014034/1103403‑1103359 .............................................CGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAGC  <  NC_014034/2330175‑2330077                                                                                                                                                  TTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTG                                            >  1:201354/1‑101 (MQ=38)  TTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGC                                           >  2:2489594/1‑101 (MQ=38)  TTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGC                                           >  1:3297153/1‑101 (MQ=38)        TGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCT                                     >  2:3737205/1‑101 (MQ=17)         GGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTC                                    >  2:1652387/1‑101 (MQ=14)             CAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCG                                >  1:1812659/1‑101 (MQ=14)                 TACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCC                            >  1:1103558/1‑101 (MQ=32)                  ACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCG                           >  2:2899445/1‑101 (MQ=32)                  ACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGAGCTCTGCGCGCCG                           >  1:2379132/1‑101 (MQ=17)                   CGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGT                          >  2:256130/1‑101 (MQ=32)                   CGCCGGGGGTGCGGGGGCGGA.CCCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGT                          <  2:2572035/101‑1 (MQ=17)                    GCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTT                         >  2:1039511/1‑101 (MQ=32)                     CCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTG                        >  2:1312382/1‑101 (MQ=32)                     CCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTG                        <  2:418331/101‑1 (MQ=32)                      CGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGC                       >  1:4156258/1‑101 (MQ=32)                      CGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGC                       >  2:3409919/1‑101 (MQ=32)                       GGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTACTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCC                      >  2:2783914/1‑101 (MQ=17)                        GGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCG                     >  1:560993/1‑101 (MQ=32)                        GGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCG                     >  1:1022193/1‑101 (MQ=32)                          ggtggGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCC                   <  1:3498758/96‑1 (MQ=17)                           gtgCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCC                  >  1:3516194/4‑101 (MQ=32)                             gCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTT                >  2:1389037/2‑101 (MQ=32)                              CGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTG               >  2:2049383/1‑101 (MQ=32)                               GGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGG              >  2:2079464/1‑101 (MQ=32)                                 gggccggcCCCCCCCCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGC             <  2:3001161/93‑1 (MQ=9)                                  GGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGG           >  2:3503630/1‑101 (MQ=31)                                  GGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGG           <  2:2486798/101‑1 (MQ=31)                                   gggcgcCCCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGG           <  2:3253346/95‑1 (MQ=0)                                   ggcggcCCCCCCCCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGG           <  2:2558201/95‑1 (MQ=0)                                   ggcgccCCCCCCCCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGG           <  1:1012506/95‑1 (MQ=0)                                   GCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGA          >  1:3030011/1‑101 (MQ=11)                                      ggcCCCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGG        <  1:1025843/98‑1 (MQ=1)                                      ggagCCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGG        >  1:2135529/5‑101 (MQ=1)                                       gagCCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGC       >  1:452511/4‑101 (MQ=1)                                         gCCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCA     >  2:3152636/2‑101 (MQ=1)                                          CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAA    >  1:3406152/1‑101 (MQ=1)                                          CCCCCCCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAA    <  1:2555321/101‑1 (MQ=1)                                            CCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAGC  <  2:1078762/101‑1 (MQ=1)                                            CCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAGC  <  1:651933/101‑1 (MQ=1)                                            CCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAGC  >  2:456194/1‑101 (MQ=1)                                                                                                                                                  TTTTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCGGAGCCCCC...................................................................................................  <  NC_014034/1103403‑1103359 .............................................CGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAGC  <  NC_014034/2330175‑2330077 Base quality scores:  ATCG  < 3 ≤  ATCG  < 21 ≤  ATCG  < 29 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG