New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1253890	28 (0.140)	36 (0.180)	3/178	32.9	0.39	intergenic (+48/+43)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
	?	NC_014034	2590190 =	86 (0.380)					intergenic (‑89/‑167)	glnE/RCAP_rcc02415	glutamate‑ammonia‑ligase adenylyltransferase/hypothetical protein
Rejected: Position hash score below cutoff.

TGGTGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGAG.........CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAAT  >  NC_014034/1253790‑1253955                                                                                                     |                                                                                tGGTGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg                                                                                 <  1:3708695/101‑1 (MQ=255) tGGTGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg                                                                                 >  2:2243434/1‑101 (MQ=255)   gTGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg.....gg                                                                          >  1:3004662/1‑101 (MQ=255)   gTGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg.....gg                                                                          <  2:1482646/101‑1 (MQ=255)    tGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg.....ggg                                                                         <  2:2829588/101‑2 (MQ=255)    tGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg.....ggg                                                                         <  1:1981245/101‑2 (MQ=255)    tGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg.....ggg                                                                         >  2:2554340/1‑100 (MQ=255)    tGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCC.AAATAACTCCGGGGGGGg.....gggg                                                                        >  1:3906139/1‑99 (MQ=255)     gCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg.....gggg                                                                        <  1:2059956/101‑3 (MQ=255)     gCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCg.....gggg                                                                        <  2:53212/101‑3 (MQ=255)       tGGGCAAGCTCGGCTTCCAGCCCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATCCCTCGGGGGTGCG.....GGGg.........cg                                                             <  1:2716882/101‑1 (MQ=255)       tGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cg                                                             <  1:99134/101‑1 (MQ=255)       tGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cg                                                             <  1:304345/101‑1 (MQ=255)        gggCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cgg                                                            <  1:2175364/101‑2 (MQ=255)         ggCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cgga                                                           <  2:1676101/101‑3 (MQ=255)         ggCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cgga                                                           <  1:3086969/101‑3 (MQ=255)         ggCAAGCTCGCCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cgga                                                           <  2:3127795/101‑3 (MQ=255)           cAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cggagc                                                         >  2:3477162/1‑97 (MQ=255)           cAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cggagc                                                         <  2:1137939/101‑5 (MQ=255)            aatcTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cggagcc                                                        <  2:2655417/98‑6 (MQ=255)            aaGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cggagcc                                                        <  1:4206463/101‑6 (MQ=255)            aaGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cggagcc                                                        <  2:2147067/101‑6 (MQ=255)             aGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cggagccc                                                       <  2:1308890/101‑7 (MQ=255)             aGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cggagccc                                                       <  2:1055339/101‑7 (MQ=255)              gCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cggagcccc                                                      >  2:1276243/1‑94 (MQ=255)              gCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cggagcccc                                                      <  2:2798068/101‑8 (MQ=255)               cTCGGCTTCCAGCCCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cggagccccc                                                     <  2:3259412/101‑9 (MQ=38)               cTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cggagccccc                                                     <  1:3929850/101‑9 (MQ=255)               cTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cggagccccc                                                     <  2:2663262/101‑9 (MQ=255)               cTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cggagccccc                                                     >  1:548740/1‑93 (MQ=255)               cTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cggagccccc                                                     >  1:2736690/1‑93 (MQ=255)               cTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cggagccccc                                                     <  2:3656738/101‑9 (MQ=255)               cTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cggagccccc                                                     <  2:511076/101‑9 (MQ=255)                 cGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGGg.........cggagcccccgc                                                   >  2:2278980/1‑91 (MQ=38)                 cGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGGGCG.....GGGg.........cggagcccccgc                                                   >  2:1656170/1‑91 (MQ=38)                                            ggCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCg                                 >  1:275792/1‑101 (MQ=12)                                              cGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGaa                               >  2:4104994/1‑101 (MQ=12)                                               gAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGaaa                              >  2:627028/1‑101 (MQ=12)                                                  aTAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATcc                           >  2:4045528/1‑101 (MQ=9)                                                    aaaCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGCGGCGAAATCctc                         >  2:103769/1‑101 (MQ=9)                                                    aaaCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGCCGCCTCGGCGAAAGCCGAGGCGAAATCctc                         >  1:2395901/1‑101 (MQ=9)                                                     aaCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCctct                        >  2:3266944/1‑101 (MQ=9)                                                     aaCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCctct                        >  2:3242456/1‑101 (MQ=9)                                                      aCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCtctc                       >  1:1827775/1‑101 (MQ=9)                                                        cGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCCGCGAAAGCCGAGGCGAAATCCTCCCAc                     >  1:2325378/1‑101 (MQ=2)                                                         gATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACg                    >  2:1324756/1‑101 (MQ=9)                                                          aTCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACgg                   >  2:425547/1‑101 (MQ=9)                                                          aTCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACgg                   >  2:2454519/1‑101 (MQ=9)                                                            cccgccccgcTCTCATCTTGCCCTAAATCCCTGGGGGGTGGG.....GGGGCGGACCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCt                 <  2:3004441/101‑1 (MQ=9)                                                            cccgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCt                 >  2:2511506/1‑101 (MQ=9)                                                              cgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTc               >  1:1068876/1‑101 (MQ=9)                                                              cgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTc               >  1:2709680/1‑101 (MQ=9)                                                               gccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTcc              >  1:2598650/1‑101 (MQ=9)                                                                ccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTGCa             >  2:1015137/1‑101 (MQ=2)                                                                ccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCa             >  1:1164426/1‑101 (MQ=9)                                                                 cccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAg            >  1:388773/1‑101 (MQ=9)                                                                   cgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGtt          >  1:3429484/1‑101 (MQ=9)                                                                      tctcATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAg       >  1:2908617/1‑101 (MQ=9)                                                                       ctcATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAgg      >  1:3149085/1‑101 (MQ=9)                                                                       ctcATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAgg      >  1:1722335/1‑101 (MQ=9)                                                                        tcATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGa     >  1:4357286/1‑101 (MQ=9)                                                                          aTCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGaaa   >  1:729813/1‑101 (MQ=9)                                                                           tCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCC.....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAAt  >  1:3488224/1‑101 (MQ=9)                                                                                                     |                                                                                TGGTGCTGGGCAAGCTCGGCTTCCAGACCGGCTGCGCCTTCGAGGCGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGAG.........CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAAT  >  NC_014034/1253790‑1253955 Base quality scores:  ATCG  < 3 ≤  ATCG  < 19 ≤  ATCG  < 26 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG