New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1103359 =	99 (0.470)	38 (0.180)	2/200	32.8	0.37	intergenic (‑359/+59)	ugpB/regA2	sn‑glycerol‑3‑phosphate‑binding periplasmic protein ugpB/photosynthetic apparatus regulatory protein RegA
	?	NC_014034	= 2330175	33 (0.160)					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                                            >  1:1565773/1‑101 (MQ=38)  TTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGC                                           >  2:174791/1‑101 (MQ=38)   TTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCG                                          >  2:158467/1‑101 (MQ=38)    TTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGG                                         >  2:3300611/1‑101 (MQ=37)    TTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGG                                         >  1:2771336/1‑101 (MQ=37)     TCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGC                                        >  1:791891/1‑101 (MQ=25)     TCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGC                                        >  1:254394/1‑101 (MQ=25)     TCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGC                                        >  1:3550770/1‑101 (MQ=25)        TGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCT                                     >  2:137965/1‑101 (MQ=17)            gCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGC                                 >  1:2508570/2‑101 (MQ=11)             CAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCG                                >  1:2927213/1‑101 (MQ=14)              AAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGC                               >  2:2662518/1‑101 (MQ=32)              AAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCCCTGCGC                               >  1:686137/1‑101 (MQ=17)                ATACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGC                             <  2:1130215/101‑1 (MQ=32)                 TACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCC                            >  1:676115/1‑101 (MQ=32)                 TACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCC                            >  1:1937040/1‑101 (MQ=32)                 TACGCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCC                            >  1:111910/1‑101 (MQ=32)                    GCCGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTT                         >  2:2471634/1‑101 (MQ=32)                      CGGGGGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGC                       >  1:3678837/1‑101 (MQ=32)                          GGTGCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCC                   >  2:804673/1‑101 (MQ=32)                            tgCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCT                 >  2:531145/3‑101 (MQ=32)                             ggGGGGGCGG.CCCCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTT                <  1:2500242/99‑1 (MQ=0)                             gCGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTT                >  1:1201300/2‑101 (MQ=32)                              gGGGGGCGGCG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTG               <  2:1376707/100‑1 (MQ=1)                              CGGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTG               >  2:2913913/1‑101 (MQ=32)                               GGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGG              >  1:612223/1‑101 (MQ=32)                               GGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGG              >  2:3896242/1‑101 (MQ=32)                               GGGGGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGG              >  2:3529538/1‑101 (MQ=32)                                  GGCGGAG.CCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGG           >  1:2267797/1‑101 (MQ=31)                                   gcgcgcCCCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGG           <  1:2374538/95‑1 (MQ=0)                                      ggagCCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGG        >  1:1738679/5‑101 (MQ=1)                                      ggagCCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGG        >  1:3210951/5‑101 (MQ=1)                                       gagCCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGC       >  2:3030/4‑101 (MQ=1)                                       gagCCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGC       >  2:2589968/4‑101 (MQ=1)                                        agCCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCC      >  1:2023306/3‑101 (MQ=1)                                         CCCCCGGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCA     <  2:938380/101‑1 (MQ=1)                                         CCCCCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCA     <  2:783732/101‑1 (MQ=1)                                            CCCGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAGC  >  1:3054466/1‑101 (MQ=1)                                                                                                                                                  TTTTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCGGAGCCCCC...................................................................................................  <  NC_014034/1103403‑1103359 .............................................CGCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAGC  <  NC_014034/2330175‑2330077 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG