New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1103359 =	148 (0.600)	57 (0.230)	7/200	25.2	0.38	intergenic (‑359/+59)	ugpB/regA2	sn‑glycerol‑3‑phosphate‑binding periplasmic protein ugpB/photosynthetic apparatus regulatory protein RegA
	?	NC_014034	= 2330175	36 (0.150)					intergenic (+150/+162)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

TTTTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCGGAGCCCCC....................................................................................................  <  NC_014034/1103403‑1103359 .............................................CG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAGC  <  NC_014034/2330175‑2330077                                                                                                                                                   TTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTG                                            >  1:4154572/1‑101 (MQ=1)  TTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGC                                           >  2:4323755/1‑101 (MQ=1)  TTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGC                                           >  2:2489664/1‑101 (MQ=1)  TTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGC                                           >  2:1962021/1‑101 (MQ=1)   TTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCG                                          >  1:4583735/1‑101 (MQ=1)    TTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGG                                         >  2:1105057/1‑101 (MQ=1)    TTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGG                                         >  1:3040680/1‑101 (MQ=1)        TGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCT                                     >  1:3967207/1‑101 (MQ=1)        TGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCT                                     >  1:4254724/1‑101 (MQ=1)          gcgCAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCT                                   >  1:480302/4‑101 (MQ=1)             CAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCG                                >  2:725545/1‑101 (MQ=1)             CAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCG                                >  1:2995122/1‑101 (MQ=1)             CAAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCG                                >  2:3496154/1‑101 (MQ=1)              AAATACGCGGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGC                               <  2:3618394/101‑1 (MQ=1)              AAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGC                               >  1:631406/1‑101 (MQ=1)              AAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGC                               >  1:81999/1‑101 (MQ=1)              AAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGC                               >  2:4447053/1‑101 (MQ=1)              AAATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGC                               >  2:4919730/1‑101 (MQ=1)               AATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCG                              >  1:669691/1‑101 (MQ=1)               AATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGGGCGGCGCTCTGCGCG                              >  2:1586182/1‑101 (MQ=1)               AATACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGGGCGGCGCTCTGCGCG                              >  1:1260472/1‑101 (MQ=1)                 TACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCC                            >  2:4125038/1‑101 (MQ=1)                 TACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCC                            >  2:90493/1‑101 (MQ=1)                 TACGCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCC                            >  1:1451432/1‑101 (MQ=1)                    GCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTT                         >  1:4072035/1‑101 (MQ=1)                    GCCGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGGCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTT                         >  1:3402427/1‑101 (MQ=1)                      CGGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGC                       >  2:1830716/1‑101 (MQ=1)                       GGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCC                      >  2:4462890/1‑101 (MQ=1)                       GGGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCC                      >  2:2863140/1‑101 (MQ=1)                       GGGGGAGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCC                      >  1:464253/1‑101 (MQ=1)                        GGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCG                     >  1:4251385/1‑101 (MQ=1)                        GGGGTGCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCG                     >  1:4154730/1‑101 (MQ=1)                             gCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTT                <  2:4562056/100‑1 (MQ=1)                             gCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTT                <  2:1953783/100‑1 (MQ=1)                             gCGGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTT                <  2:3131150/100‑1 (MQ=1)                             gCGGGGGCGCA.CCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTT                <  2:494736/100‑1 (MQ=0)                               GGGGGGGGGCCCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTG               <  2:2877786/101‑1 (MQ=0)                               GGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGGGCTCTGCGCGCCGTTGCCGCCCTTGG              >  2:741082/1‑101 (MQ=1)                               GGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGG              >  2:2559844/1‑101 (MQ=1)                               GGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGG              >  1:905673/1‑101 (MQ=1)                               GGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGG              >  2:4748093/1‑101 (MQ=1)                               GGGGGCGGAG.CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGG              >  2:1686544/1‑101 (MQ=1)                                   cgccccCCCCCCC.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGG           <  2:4254407/95‑1 (MQ=0)                                     gggcCCCCCCC.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAG         <  1:4793234/97‑1 (MQ=0)                                      ggagCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGG        >  1:1201483/5‑101 (MQ=1)                                      ggagCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGG        >  1:4081553/5‑101 (MQ=1)                                      ggagCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGG        >  2:3711830/5‑101 (MQ=1)                                      ggagCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGG        >  2:572004/5‑101 (MQ=1)                                      ggagCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGACCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGG        >  1:771653/5‑101 (MQ=1)                                         gCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCA     >  1:21854/2‑101 (MQ=1)                                         gCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCA     <  1:564971/100‑1 (MQ=1)                                         CCCCCCGCCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCC      <  2:1833358/101‑1 (MQ=0)                                         CCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCA     <  1:1180639/101‑1 (MQ=1)                                          CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAA    <  2:4047545/101‑1 (MQ=1)                                          CCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAA    <  1:4153193/101‑1 (MQ=1)                                           CCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAG   <  1:4684641/101‑1 (MQ=1)                                            CCCC.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAGC  <  2:4251068/101‑1 (MQ=1)                                                                                                                                                   TTTTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCGGAGCCCCC....................................................................................................  <  NC_014034/1103403‑1103359 .............................................CG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAGC  <  NC_014034/2330175‑2330077 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG