New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1253880	NA (NA)	59 (0.190)	10/176	30.5	0.35	intergenic (+38/+53)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
	?	NC_014034	= 2577184	224 (0.630)					intergenic (+106/‑323)	fdx/purU	ferredoxin VI/formyltetrahydrofolate deformylase
Rejected: Position hash score below cutoff.

CCGCCGCGATGGTGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGG....................................................................................................  >  NC_014034/1253781‑1253880 ....................................................................................................CGGGGGTGCGGGGGCG..GCCCCCGCCGGGTCGCCTTGGCGAAGCCAAGGCGAAACGCTTTCGCGCCCAGGCAAAAGGCCGCCCGAAGGCGGCCGTTTCATCGCGATGTCAG  <  NC_014034/2577184‑2577075                                                                                                                                                                                                                                  TGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGG                                                                                                     <  2:2675964/101‑1 (MQ=1)             TGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGG                                                                                                     <  2:2009577/101‑1 (MQ=1)             TGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGG                                                                                                     >  1:4191827/1‑101 (MQ=1)              GCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGG                                                                                                    >  2:380820/1‑101 (MQ=1)              GCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGG                                                                                                    >  1:2240352/1‑101 (MQ=1)              GCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGG                                                                                                    <  2:6904712/101‑1 (MQ=1)               CTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCTCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC                                                                                                   <  2:4863584/101‑1 (MQ=1)               CTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC                                                                                                   <  2:3388060/101‑1 (MQ=1)               CTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC                                                                                                   <  2:6583230/101‑1 (MQ=1)               CTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGC                                                                                                   >  1:4286900/1‑101 (MQ=1)               CTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCCCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGAGCGCGGGC                                                                                                   >  2:3888587/1‑101 (MQ=0)                TGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG                                                                                                  >  2:6798983/1‑101 (MQ=1)                TGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG                                                                                                  <  2:6586279/101‑1 (MQ=1)                TGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG                                                                                                  >  2:5118987/1‑101 (MQ=1)                 GGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..G                                                                                               <  2:4874665/101‑1 (MQ=1)                 GGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..G                                                                                               >  1:159875/1‑101 (MQ=1)                 GGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..G                                                                                               >  2:5088940/1‑101 (MQ=1)                  GGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Ga                                                                                              <  1:5119247/101‑2 (MQ=1)                  GGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Ga                                                                                              <  1:2607609/101‑2 (MQ=1)                   GCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gag                                                                                             >  1:2129304/1‑99 (MQ=1)                   GCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gag                                                                                             <  2:4043993/101‑3 (MQ=1)                   GCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gag                                                                                             <  1:5892588/101‑3 (MQ=1)                   GCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gag                                                                                             >  1:5686398/1‑99 (MQ=1)                   GCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gag                                                                                             <  1:5150533/101‑3 (MQ=1)                    CAAGCTCGTCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gagc                                                                                            <  2:2734914/101‑4 (MQ=1)                     AAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gagcc                                                                                           <  1:6168100/101‑5 (MQ=1)                     AAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gagac                                                                                           >  2:4426773/1‑97 (MQ=1)                     AAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTAGGGGGTGCGGGGGCG..Gagcc                                                                                           >  1:5620808/1‑97 (MQ=1)                      AGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gagccc                                                                                          <  1:5741023/101‑6 (MQ=1)                      AGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gagccc                                                                                          <  2:2941479/101‑6 (MQ=1)                       GCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gagcccc                                                                                         <  2:751006/101‑7 (MQ=1)                       GCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gagcccc                                                                                         <  2:3628615/101‑7 (MQ=1)                        CTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gagccccc                                                                                        <  2:397328/101‑8 (MQ=1)                        CTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gagccccc                                                                                        <  2:4909667/101‑8 (MQ=1)                        CTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gagccccc                                                                                        <  2:852316/101‑8 (MQ=1)                        CTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gagccccc                                                                                        <  1:5251298/101‑8 (MQ=1)                        CTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gagccccc                                                                                        <  2:2072434/101‑8 (MQ=1)                         TCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gagcccccg                                                                                       >  1:3481303/1‑93 (MQ=1)                         TCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gagcccccg                                                                                       >  1:4060888/1‑93 (MQ=1)                         TCGGCTTCCAGAACGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gagcccccg                                                                                       >  1:6308404/1‑93 (MQ=1)                          CGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCG..Gagcccccgc                                                                                      >  1:5236487/1‑92 (MQ=11)                           GGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCC                                                                                       <  2:2913461/101‑1 (MQ=31)                           GGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCC                                                                                       >  2:3081286/1‑101 (MQ=31)                           GGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCC                                                                                       >  2:3530660/1‑101 (MQ=31)                            GCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCG                                                                                      >  1:1871519/1‑101 (MQ=32)                              TTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGG                                                                                    >  2:6709396/1‑101 (MQ=32)                               TCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGc                                                                                   >  2:3389413/1‑100 (MQ=17)                                CCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTC                                                                                  >  1:4751591/1‑101 (MQ=32)                                CCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTC                                                                                  >  2:3548/1‑101 (MQ=32)                                CCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTC                                                                                  >  1:3996291/1‑101 (MQ=32)                                CCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTC                                                                                  >  1:2242155/1‑101 (MQ=32)                                  AGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGC                                                                                >  1:6170298/1‑101 (MQ=32)                                  AGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGC                                                                                >  1:23382/1‑101 (MQ=32)                                   GACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCC                                                                               >  2:4802808/1‑101 (MQ=32)                                   GACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCC                                                                               >  2:3626574/1‑101 (MQ=32)                                   GACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCC                                                                               >  2:3714570/1‑101 (MQ=32)                                    ACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCT                                                                              >  2:6161339/1‑101 (MQ=32)                                    ACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCT                                                                              >  1:2923499/1‑101 (MQ=32)                                     CCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTc                                                                             >  2:3424249/1‑100 (MQ=32)                                                                                                                                                                                                                      CCGCCGCGATGGTGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGG....................................................................................................  >  NC_014034/1253781‑1253880 ....................................................................................................CGGGGGTGCGGGGGCG..GCCCCCGCCGGGTCGCCTTGGCGAAGCCAAGGCGAAACGCTTTCGCGCCCAGGCAAAAGGCCGCCCGAAGGCGGCCGTTTCATCGCGATGTCAG  <  NC_014034/2577184‑2577075 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 29 ≤  ATCG  < 34 ≤  ATCG  < 41 ≤  ATCG