New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	985692 =	168 (0.830)	45 (0.220)	17/166	16.8	0.32	intergenic (+31/‑53)	betB/betA	betaine‑aldehyde dehydrogenase/choline dehydrogenase
	?	NC_014034	= 2330175	25 (0.100)					intergenic (+150/+162)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

TGAACCCTGTTTTTTCTTGGCGCAAATACGCCGGGGG.....................................................................................................................  <  NC_014034/985728‑985692 ......................................................CG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAGC  <  NC_014034/2330175‑2330077                                      |||||||||||||||||                                                                                                     gcgccccggcTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGG                                                      >  2:805713/11‑101 (MQ=17)  cgccccggcTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGC                                                     >  2:3213737/10‑101 (MQ=14)  ccccccggcTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGC                                                     <  2:780250/92‑1 (MQ=1)    ccccggcTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTTCTCTCCGCCATCGGCCG                                                   >  2:4653288/8‑101 (MQ=0)     cccggcTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGA                                                  <  1:1885418/95‑1 (MQ=1)     cccggcTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGA                                                  >  1:2464376/7‑101 (MQ=1)           TTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTG                                            >  1:4154572/1‑101 (MQ=1)           TTTTTCTTGGCGAAAATACGCCGGGGGGGGGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTG                                            <  2:4553042/101‑1 (MQ=0)            TTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGC                                           >  2:1962021/1‑101 (MQ=1)            TTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGC                                           >  2:2489664/1‑101 (MQ=1)            TTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGC                                           >  2:4323755/1‑101 (MQ=1)             TTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCG                                          >  1:4583735/1‑101 (MQ=1)             TTTCTTGGCGCAAATACGCCGGGGGAGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCG                                          >  2:4917797/1‑101 (MQ=1)              TTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGG                                         >  1:3040680/1‑101 (MQ=1)              TTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGG                                         >  2:1105057/1‑101 (MQ=1)              TTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCCGCCGATCCGTGCGG                                         >  2:3321482/1‑101 (MQ=1)                  TGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCTGCCATCGGCCGATCCGTGCGGCGCT                                     >  1:2130277/1‑101 (MQ=1)                  TGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCT                                     >  1:3967207/1‑101 (MQ=1)                  TGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCT                                     >  1:4254724/1‑101 (MQ=1)                    GCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCT                                   >  1:480302/1‑101 (MQ=1)                      GCAAATACGCCGGGGGGGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGC                                 <  2:4636624/101‑1 (MQ=1)                       CAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCG                                >  1:2995122/1‑101 (MQ=1)                       CAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCG                                >  2:725545/1‑101 (MQ=1)                       CAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCG                                >  2:3496154/1‑101 (MQ=1)                        AAATACGCGGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGC                               <  2:3618394/101‑1 (MQ=1)                        AAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGC                               >  2:4919730/1‑101 (MQ=1)                        AAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGC                               >  2:4447053/1‑101 (MQ=1)                        AAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGC                               >  1:631406/1‑101 (MQ=1)                        AAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGC                               >  1:81999/1‑101 (MQ=1)                        AAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGGGCGGCGCTCgccgc                               >  1:1274541/1‑96 (MQ=0)                         AATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGGGCGCTGCGCG                              >  1:3027244/1‑101 (MQ=0)                         AATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCG                              >  1:669691/1‑101 (MQ=1)                         AATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGGGCGGCGCTCTGCGCG                              >  1:1260472/1‑101 (MQ=1)                         AATACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGGGCGGCGCTCTGCGCG                              >  2:1586182/1‑101 (MQ=1)                           TACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCC                            >  2:90493/1‑101 (MQ=1)                           TACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCC                            >  2:4125038/1‑101 (MQ=1)                           TACGCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCC                            >  1:1451432/1‑101 (MQ=1)                              GCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTT                         >  1:4072035/1‑101 (MQ=1)                              GCCGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGGCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTT                         >  1:3402427/1‑101 (MQ=1)                                CGGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGC                       >  2:1830716/1‑101 (MQ=1)                                 GGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCC                      >  2:4462890/1‑101 (MQ=1)                                 GGGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCC                      >  2:2863140/1‑101 (MQ=1)                                 GGGGGAGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCC                      >  1:464253/1‑101 (MQ=1)                                  GGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCG                     >  1:4251385/1‑101 (MQ=1)                                  GGGGTGCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCG                     >  1:4154730/1‑101 (MQ=1)                                       ggGGGGGCGGCCCCCCCC.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTT                <  2:3886890/99‑1 (MQ=0)                                       GCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTT                <  2:4562056/101‑1 (MQ=1)                                       GCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTT                <  2:3131150/101‑1 (MQ=1)                                       GCGGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTT                <  2:1953783/101‑1 (MQ=1)                                       GCGGGGGCGCACCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTT                <  2:494736/101‑1 (MQ=0)                                        gGGGGGGGGCCCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTG               <  2:2877786/100‑1 (MQ=0)                                         GGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGGGCTCTGCGCGCCGTTGCCGCCCTTGG              >  2:741082/1‑101 (MQ=1)                                         GGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGG              >  1:905673/1‑101 (MQ=1)                                         GGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGG              >  2:1686544/1‑101 (MQ=1)                                         GGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGG              >  2:4748093/1‑101 (MQ=1)                                         GGGGGCGGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGG              >  2:2559844/1‑101 (MQ=1)                                            cgcccccCCCCCC.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGG           <  2:4254407/94‑1 (MQ=0)                                              gggccCCCCCC.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAG         <  1:4793234/96‑1 (MQ=0)                                               GGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGG        >  2:3711830/1‑101 (MQ=1)                                               GGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGG        >  2:572004/1‑101 (MQ=1)                                               GGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGG        >  1:4081553/1‑101 (MQ=1)                                               GGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGG        >  1:1201483/1‑101 (MQ=1)                                               GGAGCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGACCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGG        >  1:771653/1‑101 (MQ=1)                                                  cCCCCCGCCCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCC      <  2:1833358/100‑1 (MQ=0)                                                  cCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCA     <  1:1180639/100‑1 (MQ=1)                                                  GCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCA     <  1:564971/101‑1 (MQ=1)                                                  GCCCCCG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCA     >  1:21854/1‑101 (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)                                      |||||||||||||||||                                                                                                     TGAACCCTGTTTTTTCTTGGCGCAAATACGCCGGGGG.....................................................................................................................  <  NC_014034/985728‑985692 ......................................................CG.CCCGGGTCGCCGCGCCTGCGCGGCGAAATTCCTCTCCGCCATCGGCCGATCCGTGCGGCGCTCTGCGCGCCGTTGCCGCCCTTGGCGGAGGCCAAGC  <  NC_014034/2330175‑2330077 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 25 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG