New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 2330175	41 (0.190)	2 (0.010)	3/180	33.1	0.05	intergenic (+150/+162)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
	?	NC_014034	2330176 =	41 (0.180)					intergenic (+151/+161)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

CTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......CGGCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCG  >  NC_014034/2330078‑2330245                                                                                                           |                                                                      cTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......Ggg                                                                     <  1:2030083/101‑1 (MQ=255) cTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......Ggg                                                                     <  2:4400030/101‑1 (MQ=255) cTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......Ggg                                                                     >  1:3903213/1‑101 (MQ=255)  ttGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......Gggg                                                                    <  2:3436649/101‑2 (MQ=255)   tGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGCC.G.......Ggggg                                                                   >  2:3824296/1‑99 (MQ=255)    ggCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......Gggggg                                                                  >  2:1786215/1‑98 (MQ=255)      ccTCCGCCAAGGGCGGCACCGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......Ggggctcc                                                                <  2:4346917/101‑6 (MQ=255)      ccTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......Ggggctcc                                                                <  2:3974262/101‑6 (MQ=255)      ccTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......Ggggctcc                                                                <  1:73698/101‑6 (MQ=255)       cTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......Ggggggccc                                                               >  1:1961494/1‑95 (MQ=255)        tCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......Ggggctccgc                                                              <  2:3792962/101‑8 (MQ=255)        tCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......Ggggctccgc                                                              <  2:4403295/101‑8 (MQ=255)          cGCCAAGGGGGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCAGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......Ggggctccgccc                                                            <  2:1049312/101‑10 (MQ=37)          cGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......Ggggctccgccc                                                            <  2:4090765/101‑10 (MQ=38)           gCCAAGGTCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......Ggggctccgcccc                                                           <  2:3296802/101‑11 (MQ=37)           gCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......Ggggctccgcccc                                                           <  1:1887689/101‑11 (MQ=37)           gCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......Ggggctccgcccc                                                           <  2:3294478/101‑11 (MQ=37)            ccAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGCTG.......GGGCTCCGCCccc                                                           <  2:2661408/101‑1 (MQ=38)                                cAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTgcg                                             <  1:4183025/101‑1 (MQ=18)                                 agagCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTgcgc                                            <  1:4269809/101‑1 (MQ=18)                                 agagCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTgcgc                                            <  1:614274/101‑1 (MQ=18)                                   agCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCa                                          <  2:3173422/101‑1 (MQ=18)                                   agCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCa                                          <  1:2923123/101‑1 (MQ=18)                                    gccccgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCaa                                         <  1:3155748/98‑1 (MQ=18)                                     cgccgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGTCCCCGCACCCCCGGCGTATTTGCGCCAAg                                        <  2:3902959/101‑1 (MQ=21)                                     cgccgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAg                                        <  1:3367409/101‑1 (MQ=18)                                     cgccgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAg                                        <  2:3723166/101‑1 (MQ=18)                                       ccgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGaa                                      <  1:1377464/101‑1 (MQ=18)                                        cgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGaaa                                     <  1:3363685/101‑1 (MQ=18)                                          cACGGATCGGCCGATTGTGGAGAGGAATTTCGCCGCGCAGGCGCGGCGTCCCGGGC.GGGGGCTCCGCCCCCGCTCCCCCGGCGTATTTGCGCCAAGaaaaa                                   <  1:3690095/101‑1 (MQ=12)                                          cACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCCCCCCCGGCGTATTTGCGCCAAGaaaaa                                   <  2:500791/101‑1 (MQ=17)                                          cACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGaaaaa                                   <  2:3567426/101‑1 (MQ=17)                                            cGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGc                                 <  1:3710638/101‑1 (MQ=18)                                             ggttgggCCTATGGCGGAGAGGAATTTCGCCTCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGcc                                <  1:3142471/96‑1 (MQ=9)                                             ggATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGcc                                <  2:2661258/101‑1 (MQ=18)                                             ggATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGcc                                <  1:2692365/101‑1 (MQ=18)                                                   gCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGgcg                          <  1:1572619/101‑1 (MQ=17)                                                   gCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGgcg                          <  2:4341996/101‑1 (MQ=17)                                                    ccGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGgcgc                         <  1:2169334/101‑1 (MQ=17)                                                    ccGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCCCACCCCCGGCGTATTTGCGCCAAGAAAAAAACGGGgcgc                         >  1:191330/1‑101 (MQ=9)                                                     cGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGgcgcg                        <  2:3020424/101‑1 (MQ=17)                                                     cGATGGCGCAGAGGCATTTCGCCGCGCAGGCGCAGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGgcgcg                        <  1:3848669/101‑1 (MQ=9)                                                        tGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCAt                     <  1:4005371/101‑1 (MQ=17)                                                        tGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCAt                     <  1:2744976/101‑1 (MQ=17)                                                         ggCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATg                    >  1:3254901/1‑101 (MQ=17)                                                         ggCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATg                    <  1:684923/101‑1 (MQ=17)                                                            ggAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCGCCCCCGGCGTATTTGCGCTAAGAAAAAGCCGGGGCGCGCATGCgg                 <  1:888535/101‑1 (MQ=12)                                                            ggAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCgg                 <  2:340920/101‑1 (MQ=17)                                                            ggAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCga                 <  2:3456097/101‑2 (MQ=17)                                                             gagaGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCggg                <  2:2559754/101‑1 (MQ=17)                                                             gagaGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCggg                >  2:4233911/1‑101 (MQ=17)                                                                  gAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGcccc           <  2:1961365/101‑1 (MQ=17)                                                                  gAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGcccc           >  2:1288734/1‑101 (MQ=17)                                                                  gAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGCGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGcccc           <  2:2521389/101‑1 (MQ=18)                                                                    aTTTCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCgg         <  1:1619891/101‑1 (MQ=17)                                                                       tCGCCGCGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATc      <  2:2522010/101‑1 (MQ=18)                                                                        cgccgcGCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCa     <  2:928724/101‑1 (MQ=18)                                                                           cgcgCAGGCGCGGCGACCCGGGC.GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACcg  <  2:1168758/101‑1 (MQ=18)                                                                                                           |                                                                      CTTGGCCTCCGCCAAGGGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC.G.......CGGCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCG  >  NC_014034/2330078‑2330245 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG