New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	2330179 =	45 (0.200)	17 (0.080)	6/154	33.7	0.18	intergenic (+154/+158)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
	?	NC_014034	= 2577171	106 (0.360)					intergenic (+93/‑336)	fdx/purU	ferredoxin VI/formyltetrahydrofolate deformylase
Rejected: Position hash score below cutoff.

GGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....G.......CG...G.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAT  >  NC_014034/2330094‑2330279                                                                                                           |                                                                                                     ggcggcAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....G.......GG...G.......GCGCCCCccccccccc                                                                                       >  2:4398889/1‑97 (MQ=37)               gcAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTgc                                                                                <  1:3431087/101‑1 (MQ=18)                    gcgcCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCaa                                                                           <  1:325766/101‑1 (MQ=18)                     cgccgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAg                                                                          >  1:1540157/1‑101 (MQ=18)                     cgccgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAg                                                                          <  1:3748960/101‑1 (MQ=18)                      gccgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCCCCCCCGGCGCATTTGCGCCAAGa                                                                         >  2:3681189/1‑101 (MQ=16)                       ccgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaa                                                                        <  2:2087225/101‑1 (MQ=18)                       ccgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaa                                                                        <  1:4810460/101‑1 (MQ=18)                        cgcACGGATCGGCCGATGGCTGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaaa                                                                       <  2:2288969/101‑1 (MQ=17)                        cgcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaaa                                                                       <  1:1355969/101‑1 (MQ=18)                         gcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaaaa                                                                      <  2:2915047/101‑1 (MQ=18)                         gcACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaaaa                                                                      <  2:1597412/101‑1 (MQ=18)                          cACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaaaaa                                                                     <  1:5524385/101‑1 (MQ=17)                          cACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGaaaaa                                                                     <  2:155248/101‑1 (MQ=17)                             ggATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....G.......GG...GGCTCCCCCCCCGCACCCCCGGCGTATTTTCGCCACGAAAAAAcc                                                                  >  2:2703774/1‑101 (MQ=16)                              gATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCg                                                                 <  2:2923180/101‑1 (MQ=18)                              gATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCg                                                                 <  2:2268564/101‑1 (MQ=18)                              gATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCCCCG...C.......CCCCGCACCCCCCGCGTACTTTCGCCAAGAAAAAACCg                                                                 >  2:2592446/1‑101 (MQ=16)                               aTCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCgg                                                                <  2:1453645/101‑1 (MQ=18)                                tCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCggg                                                               <  1:3521070/101‑1 (MQ=18)                                tCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCggg                                                               <  1:1468629/101‑1 (MQ=18)                                tCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCggg                                                               <  1:542692/101‑1 (MQ=18)                                tCGGCAGAGGGGGGAAAGGATTTGCGCCGCGCAGGCGCGGCGCCCCGGGCTGGGG.......CGCCCC.......CCCCGCCCCCCCGGCTTATTTGCCCCAAGAAAAAGCCggg                                                               <  2:3297111/101‑1 (MQ=255)                                  ggCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGgc                                                             <  2:4312940/101‑1 (MQ=17)                                  ggCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCCCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGgc                                                             >  2:1389521/1‑101 (MQ=17)                                   gCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGgcg                                                            <  2:4646881/101‑1 (MQ=17)                                     cGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGgcgcg                                                          <  1:3851443/101‑1 (MQ=17)                                     cGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGgcgcg                                                          <  1:5385709/101‑1 (MQ=17)                                        tGGCGGAGAGGAATTTCGCCGCGCAGGCGCCGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCAt                                                       <  1:2191189/101‑1 (MQ=17)                                         ggCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATg                                                      <  1:843808/101‑1 (MQ=17)                                         ggCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATg                                                      <  2:3104092/101‑1 (MQ=17)                                         ggCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATg                                                      <  1:3336555/101‑1 (MQ=17)                                           cGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCg                                                    <  1:443443/101‑1 (MQ=18)                                               gagGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGc                                                <  1:4475972/101‑1 (MQ=18)                                                 ggAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGccc                                              <  1:2775699/101‑1 (MQ=17)                                                  gAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGcccc                                             <  1:4174848/101‑1 (MQ=17)                                                  gAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGcccc                                             <  1:2428997/101‑1 (MQ=17)                                                    aTTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCgg                                           <  2:1137243/101‑1 (MQ=17)                                                    aTTTCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCgg                                           >  2:194945/1‑101 (MQ=17)                                                      tgcgccgcGCGGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGAt                                         <  1:5348728/99‑1 (MQ=12)                                                       tCGCCGCGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATc                                        <  2:4035527/101‑1 (MQ=18)                                                         gccgcGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCAc                                      <  2:236734/101‑1 (MQ=18)                                                         gccgcGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCAc                                      <  2:1619744/101‑1 (MQ=18)                                                          ccgcGCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCAcc                                     <  1:4913597/101‑1 (MQ=18)                                                           cgcgCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACcg                                    >  2:4571424/1‑101 (MQ=18)                                                           cgcgCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACcg                                    <  1:3696609/101‑1 (MQ=18)                                                           cgcgCAGGCGCGGCGACCCGGGC....GGGGGCTCCG...C.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACcg                                    <  1:1041180/101‑1 (MQ=18)                                                                                                 ggggctccgcccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTgg            >  1:3977034/11‑101 (MQ=255)                                                                                                   ggctccgcccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTgggg          >  2:2258463/9‑101 (MQ=255)                                                                                                     ctccgcccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCCTGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGcc        >  1:4482486/7‑101 (MQ=255)                                                                                                      tccgcccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCa       >  1:3318967/6‑101 (MQ=255)                                                                                                       ccgcccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCaa      <  1:5355730/97‑1 (MQ=255)                                                                                                        cgcccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCaaa     <  2:4116355/98‑1 (MQ=255)                                                                                                         gcccccGCACCCCCGGCGTATTTGCGCCAAGAAGAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAg    <  1:4940906/99‑1 (MQ=255)                                                                                                         gcccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCaaaa    >  1:4715826/3‑100 (MQ=255)                                                                                                          cccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGa   >  2:2344058/2‑101 (MQ=255)                                                                                                          cccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGa   <  2:4863193/100‑1 (MQ=255)                                                                                                           ccccGCACCCCCGGCGTATTTGCGCCAAGAGAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAt  >  1:757145/1‑101 (MQ=255)                                                                                                           ccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAt  >  1:1325877/1‑101 (MQ=255)                                                                                                           ccccGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCAAGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAt  >  2:5008610/1‑101 (MQ=255)                                                                                                           |                                                                                                     GGCGGCAACGGCGCGCAGAGCGCCGCACGGATCGGCCGATGGCGGAGAGGAATTTCGCCGCGCAGGCGCGGCGACCCGGGC....G.......CG...G.......CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGAT  >  NC_014034/2330094‑2330279 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 29 ≤  ATCG  < 34 ≤  ATCG  < 41 ≤  ATCG