New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 432507	167 (0.800)	51 (0.240)	21/176	21.3	0.33	intergenic (+110/+38)	RCAP_rcc00403/RCAP_rcc00404	hypothetical protein/Sua5/YciO/YrdC/YwlC family protein
	?	NC_014034	1640006 =	42 (0.180)					intergenic (+86/‑59)	mccB/mccA	methylcrotonoyl‑CoA carboxylase subunit beta/methylcrotonoyl‑CoA carboxylase subunit alpha
Rejected: Position hash score below cutoff.

CCGGGCTTCGTTTCATCTTGCCCCAAATATCCCGGGGG...............................................................................................................  >  NC_014034/432470‑432507 ..................................................GCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGGCCGAGATCG  >  NC_014034/1640006‑1640104                                       ||||||||||||                                                                                                    aacccatcccTTTCATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGG                                                  >  1:3136026/11‑101 (MQ=37) aacccatcccTTTCATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGG                                                  >  2:4326659/11‑101 (MQ=37)    ccatcccTTTCATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGA                                               >  1:2833371/8‑101 (MQ=33)      atcccTTTCATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACC                                             >  2:2914303/6‑101 (MQ=31)      atcccTTTCATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACC                                             >  1:2122948/6‑101 (MQ=31)       tcccTTTCATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCG                                            >  1:83676/5‑101 (MQ=11)       tcccTTTCATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCG                                            >  1:3846642/5‑101 (MQ=11)         ccTTTCATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGCAGGAGACCGCG                                          >  2:1603274/3‑101 (MQ=1)         ccTTTCATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCG                                          >  1:1338230/3‑101 (MQ=1)         ccTTTCATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCG                                          >  1:3621634/3‑101 (MQ=1)         ccTTTCATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCG                                          >  1:2002142/3‑101 (MQ=1)          cTTTCATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCGCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGA                                         >  2:4028967/2‑101 (MQ=1)           TTTCATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGAT                                        >  1:444767/1‑101 (MQ=1)            TTCATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCGGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATG                                       >  2:976288/1‑101 (MQ=1)             TCATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGT                                      >  2:3346597/1‑101 (MQ=1)             TCATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGT                                      >  2:3558206/1‑101 (MQ=1)             TCATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGT                                      >  2:3796993/1‑101 (MQ=1)             TCATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGT                                      >  1:3649654/1‑101 (MQ=1)              CATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTT                                     >  1:3058043/1‑101 (MQ=1)              CATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTT                                     >  2:3897908/1‑101 (MQ=1)              CATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTT                                     >  2:4469830/1‑101 (MQ=1)               ATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTT                                    >  1:1349631/1‑101 (MQ=1)               ATCTTGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCCCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTT                                    >  1:1897689/1‑101 (MQ=1)                   TGCCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAA                                >  1:1549628/1‑101 (MQ=1)                     CCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAG                              >  1:2541920/1‑101 (MQ=1)                     CCCCAAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCAGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAG                              >  2:3654005/1‑101 (MQ=1)                         AAATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCC                          >  1:1182454/1‑101 (MQ=1)                          AATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCT                         >  2:2849596/1‑101 (MQ=1)                          AATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCT                         >  1:695372/1‑101 (MQ=1)                           ATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTG                        >  2:449998/1‑101 (MQ=1)                           ATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTG                        >  2:3511336/1‑101 (MQ=1)                           ATATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTG                        >  2:645818/1‑101 (MQ=1)                            TATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGA                       >  1:3437014/1‑101 (MQ=1)                             ATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGAT                      >  1:1884789/1‑101 (MQ=1)                             ATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGAT                      >  2:2788189/1‑101 (MQ=1)                             ATCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGGTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGAc                      >  2:3661330/1‑100 (MQ=1)                              TCCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGAGGAAGGAGACCGCGATGTTTCAAAAGATCCTGATC                     >  1:4002554/1‑101 (MQ=1)                               CCCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCG                    >  1:3028055/1‑101 (MQ=1)                                CCGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGC                   >  1:1907525/1‑101 (MQ=1)                                 CGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTNAAAAGATCCTGATCGCC                  >  2:892503/1‑101 (MQ=1)                                 CGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCC                  >  1:4382835/1‑101 (MQ=1)                                 CGGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCC                  >  2:4353945/1‑101 (MQ=1)                                  GGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCA                 >  1:2626144/1‑101 (MQ=1)                                  GGGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCA                 >  1:1210783/1‑101 (MQ=1)                                   GGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAA                >  1:2475538/1‑101 (MQ=1)                                   GGGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCCCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAA                >  1:4478553/1‑101 (MQ=1)                                    GGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAAC               >  1:804821/1‑101 (MQ=1)                                    GGGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCCCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGAAGTTTCAAAAAATCCTGATCGCCAAa               >  1:1045882/1‑100 (MQ=0)                                     GGGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACA              >  2:1400708/1‑101 (MQ=1)                                      GGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAG             >  2:4437627/1‑101 (MQ=1)                                      GGCCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAG             >  1:483894/1‑101 (MQ=1)                                        CCCGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGG           >  2:2302728/1‑101 (MQ=1)                                          gGGGGGGCCCCCCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGGCC         <  1:2944500/100‑1 (MQ=0)                                          CGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGGCC         >  2:938051/1‑101 (MQ=1)                                          CGGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGGCC         >  1:2995333/1‑101 (MQ=1)                                           GGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGGCCG        >  1:1753373/1‑101 (MQ=1)                                           GGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGGCCG        >  2:4586190/1‑101 (MQ=1)                                           GGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGGCCG        >  1:2394281/1‑101 (MQ=1)                                           GGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGGCCG        >  1:2907105/1‑101 (MQ=1)                                           GGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGGCCG        >  1:3827010/1‑101 (MQ=1)                                           GGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGGCCG        >  2:112525/1‑101 (MQ=1)                                           GGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGGCCG        >  1:733607/1‑101 (MQ=1)                                           GGGGGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGGCCG        >  1:991799/1‑101 (MQ=1)                                              GGGCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGGCCGAGA     >  1:2811728/1‑101 (MQ=1)                                               GGCCGCCCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGGCCGAGAT    <  1:1973800/101‑1 (MQ=0)                                                GCAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGGCCGAGATC   >  1:325783/1‑101 (MQ=1)                                                 CAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGGCCGAGATCG  >  2:1192324/1‑101 (MQ=1)                                                 CAGCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGGCCGAGATCG  >  2:3318101/1‑101 (MQ=1)                                       ||||||||||||                                                                                                    CCGGGCTTCGTTTCATCTTGCCCCAAATATCCCGGGGG...............................................................................................................  >  NC_014034/432470‑432507 ..................................................GCGCCCCCCGCCACTTCCGCCACGGGGCAGCGCCCCGGCCGTTGACGAAGGAGACCGCGATGTTTCAAAAGATCCTGATCGCCAACAGGGCCGAGATCG  >  NC_014034/1640006‑1640104 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 38 ≤  ATCG