New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 158254	210 (0.490)	37 (0.090)	4/188	39.1	0.24	intergenic (+57/‑173)	parC/tuf1	DNA topoisomerase IV subunit A/translation elongation factor Tu
	?	NC_014034	= 974301	22 (0.050)					intergenic (+181/+78)	RCAP_rcc00884/RCAP_rcc00885	hypothetical protein/hypothetical protein
Rejected: Position hash score below cutoff.

CCCCCCGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CG.TGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.GGGG...T...GTGCG.....GAAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGCGAAATACCCCCGCCGCAACGGCCGGTTCTCAG  >  NC_014034/974202‑974382                                                                                                      |                                                                                               ccccccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGCTTTCCCCCTGCCCCAAAAATc                                                                                                >  1:8973320/1‑101 (MQ=37)  tggctgggccccccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGGTTTTACCTTGCGACAAATATcc                                                                                               >  2:3642145/9‑101 (MQ=38)  cccgcGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATcc                                                                                               <  2:1539862/101‑1 (MQ=255)  cccccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATcc                                                                                               <  2:7133605/101‑1 (MQ=255)  cccccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATcc                                                                                               <  1:6993198/101‑1 (MQ=255)   ccccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCCCCTTGCGGCAAATATcc.c                                                                                             >  1:6850228/1‑101 (MQ=39)   ccccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATcc.c                                                                                             >  1:1392318/1‑101 (MQ=255)   ccccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATcc.c                                                                                             >  1:4568230/1‑101 (MQ=255)    cccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.g                                                                                           >  1:8296522/1‑101 (MQ=255)     ccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTTACCTTGCGACACATATcc.ccg                                                                                           >  2:6157328/1‑99 (MQ=38)     ccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTTACCTTGCGACAAATATcc.ccg                                                                                           >  1:5115438/1‑99 (MQ=255)     ccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATcc.ccg                                                                                           >  1:3592506/1‑99 (MQ=255)     ccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCCTGTCGCAAATATtc.ccg                                                                                           >  2:3204601/1‑99 (MQ=37)      cGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.ggg                                                                                         >  2:9160570/1‑101 (MQ=255)      cGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAAAATCC.C.ggg                                                                                         >  1:4896942/1‑101 (MQ=255)       ggACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTTCCCTTGCGAACAATATCC.C.gggg                                                                                        >  2:2677963/1‑101 (MQ=38)       ggACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCCCCCTTCGACAAATATAC.C.cggg                                                                                        >  1:1077670/1‑101 (MQ=37)       ggACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATTC.C.gggg                                                                                        >  2:6143285/1‑101 (MQ=255)       ggACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggg                                                                                        >  2:1447569/1‑101 (MQ=255)        gACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.ggggg                                                                                       >  2:7845050/1‑100 (MQ=255)        gACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.ggggg                                                                                       >  2:6884226/1‑100 (MQ=255)        gACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.ggggg                                                                                       >  1:7113758/1‑100 (MQ=255)        gACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.ggggg                                                                                       <  1:6958062/101‑2 (MQ=255)        gACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.ggggg                                                                                       >  1:4832796/1‑100 (MQ=255)        gACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.ggggg                                                                                       >  1:4545441/1‑100 (MQ=255)        gACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.cgggg                                                                                       >  1:715269/1‑100 (MQ=255)         gccccccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggt                                                                                      <  2:8972899/100‑3 (MQ=255)         aCCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.cggggt                                                                                      >  2:1725297/1‑99 (MQ=255)          ccccccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtc                                                                                     <  1:4571081/101‑4 (MQ=255)          ccccccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtc                                                                                     <  1:2358036/101‑4 (MQ=255)          ccccccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtc                                                                                     <  2:4873486/101‑4 (MQ=255)          ccccccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.cggggtc                                                                                     >  1:2323734/1‑98 (MQ=38)           cccccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtcc                                                                                    <  1:6143522/101‑5 (MQ=255)           cccccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtcc                                                                                    <  1:1725350/101‑5 (MQ=255)            ccccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtccg                                                                                   <  1:6841177/101‑6 (MQ=255)             cccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtccgg                                                                                  <  2:7756647/101‑7 (MQ=39)             cccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtccgg                                                                                  <  2:4896782/101‑7 (MQ=39)             cccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtccgg                                                                                  <  2:3485095/101‑7 (MQ=39)             cccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.cggggtccgg                                                                                  >  1:1339272/1‑95 (MQ=38)              ccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTTACCTTGCGACAAATATCC.C.ggggggccggg                                                                                 >  1:86867/1‑94 (MQ=38)               cAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtccgggg                                                                                <  2:313528/101‑9 (MQ=38)                 gCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtccgggggc                                                                              <  1:727450/101‑11 (MQ=38)                 gCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtccgggggc                                                                              <  2:2323667/101‑11 (MQ=38)                 gCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.ggggggccgggggc                                                                              >  1:2085746/1‑91 (MQ=38)                                      gCAGCCGGGCGGGATGCGCAATGCC.CGCTGCGCAGCGGCTTGTTTACACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCt                                                  <  2:9111592/101‑1 (MQ=0)                                        agccgggcgggATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATA.CC.C.GGGG...G...GTCCGGGGGCGGAGCCCCCGGCGGGTCGCCTCg                                                <  2:6849956/98‑1 (MQ=9)                                               cgggACCCGGCATGGCGTC.TGGGCGGCGGCTTTTTTTCTCCTTGCGACAAATACCC.CGGGGG...TCC.GGGGGC....GGACCCCCCGGCGGGTCGCCTCGGCGACAg                                         <  1:8484935/101‑1 (MQ=2)                                                  gATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCCCCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCg                                      <  1:2806748/101‑1 (MQ=9)                                                    tCCGTCATGGC.CGCTGCACAGCGGCTTGTTTTCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAg                                    <  2:1611338/101‑1 (MQ=2)                                                    tCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAg                                    <  2:2486427/101‑1 (MQ=11)                                                      cGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCCGG.GGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGc                                  <  2:3760642/101‑1 (MQ=2)                                                      cGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGc                                  <  1:1641537/101‑1 (MQ=11)                                                          aTGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGCGaaa                              <  2:3424245/101‑1 (MQ=11)                                                              gccgctGCGCAGCGGCTTGTATTCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACTGCCGAGGCGCACTAc                           <  1:8834430/96‑1 (MQ=2)                                                                 gctGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGCGAAATAcccc                        <  2:4958861/99‑1 (MQ=11)                                                                     cgcACCGGCTTGTTTCCCCCTGGCGACAAATATCCGG.GGGG...TCG.GGGGGC....GGACCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGCGAAATACCCcggcc                    <  2:5815710/101‑1 (MQ=2)                                                                           ggCTTGTTTTCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGCGAAATACCCCGGCCGCAACg              <  2:7252201/101‑1 (MQ=11)                                                                             tttGTTTCCGCCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGCGAAATACCCCGGCCGCAACGGc            <  1:6945617/100‑1 (MQ=2)                                                                              ttGTTTTCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGGCGCCGCCGCGGCCGCCGCGGGGGAAAACACCCGCCCCCACCGcc           >  2:6319615/1‑101 (MQ=0)                                                                               tGTTTTCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGGGGGCGCGGCGGCAGCCGCGGGGGAATAACCCCCCCCCACCGGCCg          >  2:6888089/1‑101 (MQ=0)                                                                                   ttCACCTTGCGACAAATATCC.CGGGGG...TCCGGTGGC.....GGAGCCCCCGGCGGGGGGCGCCGGCGCCAGACGGGGCGGAAGAAACCGGCCGCAACGGCCggggg      >  1:1533918/1‑98 (MQ=0)                                                                                    tCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGGGGCCTCGGCGGCCGCCGCGGGGGAAGAACCCCGCCGCCACCGCCGGGtct     >  1:1807081/1‑101 (MQ=2)                                                                                    tCACCTTGCGACAAATAGCC.C.GGGGGGCC...GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGCGAAATACCCCGGCCGCAACGGCCGGTtct     <  1:5294916/101‑1 (MQ=2)                                                                                     cACCTTGCGACAAATATCC.G.GGGGGCCC...GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGCGAAATACCCCGGCCGCAACGGCCGGTtctc    <  2:1469899/101‑1 (MQ=2)                                                                                     cACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGGCGGCCCGGCGACCGCCGCGGCGGAAAACCCCGGCCGCCCCGGcacggtcgc    >  2:8178717/1‑93 (MQ=2)                                                                                       ccTTGCGACAAATATCC.CGGGGG...TCCGGGGGC.....GGAGCCCCCGGCGGGGGGCCTCGGGGGCAGCCGCGGCGGAAAAACACCGCCGCCCCAGCCgggcccccc  >  2:3614922/1‑94 (MQ=2)                                                                                                      |                                                                                               CCCCCCGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CG.TGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.GGGG...T...GTGCG.....GAAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGCGAAATACCCCCGCCGCAACGGCCGGTTCTCAG  >  NC_014034/974202‑974382 Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 25 ≤  ATCG  < 34 ≤  ATCG  < 41 ≤  ATCG