New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1253892	42 (0.150)	47 (0.170)	16/192	30.6	0.41	intergenic (+50/+41)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
	?	NC_014034	3276377 =	94 (0.320)					intergenic (‑129/+120)	RCAP_rcc03082/RCAP_rcc03083	lipoprotein/membrane bound YbgT‑like protein
Rejected: Position hash score below cutoff.

GTGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGAG....C....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAAT  >  NC_014034/1253792‑1253955                                                                                                          |                                                                        gTGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGACCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg.....gg                                                                         <  2:4129617/101‑1 (MQ=255)  tGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg.....ggg                                                                        <  1:3721486/101‑2 (MQ=255)   gCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg.....gggg                                                                       <  1:1648087/101‑3 (MQ=255)   gCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg.....gggg                                                                       >  2:3610669/1‑99 (MQ=255)    cTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTACATACCTCGGGGGTGCG.....GGGg....c                                                                  <  1:3287476/101‑1 (MQ=255)    cTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c                                                                  <  2:5495142/101‑1 (MQ=255)     tGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....g                                                             <  2:2879266/101‑1 (MQ=255)      gggCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....gg                                                            <  1:2768421/101‑2 (MQ=255)       ggCAAGCTCGGCTTCCAGGCCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....gga                                                           <  1:4407218/101‑3 (MQ=255)         cAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagc                                                         <  2:2296930/101‑5 (MQ=255)         cAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagc                                                         >  2:5655651/1‑97 (MQ=255)         cAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagc                                                         >  2:4237004/1‑97 (MQ=255)         cAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagc                                                         <  1:604756/101‑5 (MQ=255)         cAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagc                                                         >  2:4540525/1‑97 (MQ=255)          aaGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagcc                                                        >  2:4611253/1‑96 (MQ=255)          aaGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagcc                                                        <  2:2659941/101‑6 (MQ=255)          aaGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGGGCG.....GGGg....c....ggagcc                                                        >  1:5707759/1‑96 (MQ=255)          aaGCTCGGCTTCCAGACCGGCTGAGCCTTGGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagcc                                                        <  1:1623746/101‑6 (MQ=38)           aGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagccc                                                       >  1:5609830/1‑95 (MQ=255)           aGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagccc                                                       <  2:184310/101‑7 (MQ=255)            gCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagcccc                                                      >  1:867335/1‑94 (MQ=255)             cTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAACCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagccccc                                                     <  2:3528109/101‑9 (MQ=38)             cTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....gggcccacc                                                     >  2:1269995/1‑93 (MQ=255)             cTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagccccc                                                     <  2:5185018/101‑9 (MQ=255)             cTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagcccca                                                     <  1:620523/101‑9 (MQ=255)              tCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagcccccg                                                    >  1:3619821/1‑92 (MQ=38)              tCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagcccccg                                                    >  1:3367476/1‑92 (MQ=38)              tCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg....c....ggagcccccg                                                    >  2:650778/1‑92 (MQ=38)                                          ggCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCg                                 >  2:5356405/1‑101 (MQ=9)                                          ggCAAAAAAACCCGACCCCGCCCCGCTCTCATCTTCCCCTAAATCCCTGGGGGGTGGGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCg                                 <  2:5065266/101‑1 (MQ=2)                                              aaaTAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAAt                             >  1:2926960/1‑101 (MQ=9)                                               aaTAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATc                            >  2:3570127/1‑101 (MQ=9)                                                  aaaCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCctc                         >  1:5486119/1‑101 (MQ=9)                                                  aaaCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCctc                         >  1:5167136/1‑101 (MQ=9)                                                  aaaCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCctc                         >  2:2042639/1‑101 (MQ=9)                                                     ccGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCa                      >  1:2946857/1‑101 (MQ=9)                                                      cGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCAc                     >  1:525419/1‑101 (MQ=9)                                                      cGACCCCCCCCCTCTCTCATCTTGCCCTAAATCCCCGGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCAc                     <  2:870099/101‑1 (MQ=2)                                                       gATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACg                    >  2:1658746/1‑101 (MQ=9)                                                       gATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACg                    >  2:1501532/1‑101 (MQ=9)                                                       gATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACg                    >  1:1645515/1‑101 (MQ=9)                                                         tCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGc                  >  1:4579903/1‑101 (MQ=9)                                                          cccgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCt                 >  2:2974796/1‑101 (MQ=9)                                                           ccgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGGAATCCTCTCACGCCtt                >  1:5039673/1‑101 (MQ=9)                                                           ccgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCtt                >  2:5771562/1‑101 (MQ=9)                                                           ccgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCtt                >  1:1521849/1‑101 (MQ=9)                                                           ccgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCtt                >  2:714134/1‑101 (MQ=9)                                                           ccgccccgcTCTCATCTTGCCCTAAATACCCCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCtt                >  1:5140933/1‑101 (MQ=2)                                                            cgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTc               >  1:1668561/1‑101 (MQ=9)                                                            cgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGATTc               >  2:4096463/1‑101 (MQ=9)                                                             gccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTcc              >  1:3676071/1‑101 (MQ=9)                                                             gccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTcc              >  2:3372749/1‑101 (MQ=9)                                                              ccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCa             >  2:4176033/1‑101 (MQ=9)                                                               cccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGGTTCCAg            >  2:1086953/1‑101 (MQ=9)                                                                 cgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGtt          >  2:1218679/1‑101 (MQ=9)                                                                  tctctCATCTTGCCCTAAATCCCTCGGGGGTGCGGGGGCGGAG....CCCCTGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTc         <  2:2245326/100‑1 (MQ=9)                                                                  gcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTc         >  1:4297163/1‑101 (MQ=9)                                                                  gcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTc         >  1:4844535/1‑101 (MQ=9)                                                                  gcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTc         >  1:2828355/1‑101 (MQ=9)                                                                   ctctCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCa        >  2:5198937/1‑101 (MQ=9)                                                                   ctctCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCa        >  1:159353/1‑101 (MQ=9)                                                                     ctcATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTTCAGTTCAgg      >  1:2858633/1‑101 (MQ=9)                                                                      tcATCTTGCCCTAAATACCTCGGGGGCGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGGGAAATCCTCTCACGGCCTCCCGTTcccga     >  1:1301957/1‑97 (MQ=0)                                                                       cATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGaa    >  2:435806/1‑101 (MQ=9)                                                                       cATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGaa    >  1:5399624/1‑101 (MQ=9)                                                                       cATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGaa    >  2:1531976/1‑101 (MQ=9)                                                                        aTCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGaaa   >  1:108653/1‑101 (MQ=9)                                                                        aTCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGaaa   >  2:667047/1‑101 (MQ=9)                                                                        aTCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGaaa   >  2:4410206/1‑101 (MQ=9)                                                                         tCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCC....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAAt  >  2:4333009/1‑101 (MQ=9)                                                                                                          |                                                                        GTGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGAG....C....GCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAAT  >  NC_014034/1253792‑1253955 Base quality scores:  ATCG  < 3 ≤  ATCG  < 17 ≤  ATCG  < 24 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG