New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1478647	169 (0.790)	61 (0.280)	21/190	21.0	0.41	intergenic (+135/+8)	RCAP_rcc01372/RCAP_rcc01373	ABC transporter ATP‑binding protein/RpiR family transcriptional regulator
	?	NC_014034	2600957 =	7 (0.030)					intergenic (+19/‑122)	RCAP_rcc02424/surE	short‑chain dehydrogenase/reductase family oxidoreductase/5'‑nucleotidase SurE
Rejected: Position hash score below cutoff.

TTGGAGCAAGATGAAAGCACGATCTGCGGTTTTCATTTATCTTGCTTCAAATATCCCGGGGGGTGAATTGGCCGAGAGGGC.AAGAGGGGGCAGCGCCCCCT....................................................................................................  >  NC_014034/1478547‑1478647 .................................................................................................CCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGCGGCTAATCAGACA  >  NC_014034/2600957‑2601056                                                                                                                                                                                                                                                                       GGGGTGAATTGGCCAA.AGGCC.AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGC                                          >  1:611794/1‑101 (MQ=255)                                                            GGGGTGAATTGGCC.AAAGGCC.AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGC                                          <  1:3311869/101‑1 (MQ=255)                                                              GGTGAATTGGCCAA.AGGCC.AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGG                                        >  1:2731941/1‑101 (MQ=255)                                                               GTGAATTGGCC.AAAGGCC.AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGC                                       >  2:2376447/1‑101 (MQ=255)                                                                   ATTGGCC.AAAGGCC.AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGC                                   >  2:2609212/1‑101 (MQ=9)                                                                   ATTGGCC.AAAGGCC.AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGC                                   >  1:3238268/1‑101 (MQ=9)                                                                       ggccaaAGGCC.AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTG                                >  2:3902543/7‑101 (MQ=2)                                                                       ggccaaAGGCC.AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTG                                <  1:4437761/95‑1 (MQ=2)                                                                         gccaAGGGCAAAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGT                               <  2:3352361/97‑1 (MQ=0)                                                                         ccaaAGGCC.AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGGTTGTT                              >  2:1475352/5‑101 (MQ=2)                                                                         ccaaAGGCC.AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTT                              >  1:1550426/5‑101 (MQ=2)                                                                          caaAGGCC.AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTT                             <  2:2849065/98‑1 (MQ=2)                                                                           aaAGGCC.AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTG                            >  2:638660/3‑101 (MQ=11)                                                                            aAGGCC.AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGG                           >  2:2708089/2‑101 (MQ=11)                                                                              ggcC.AAGAGGGGGCAGCCCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCT                         <  1:1328676/98‑1 (MQ=2)                                                                               ggccagGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCT                         <  1:3902797/95‑1 (MQ=0)                                                                               gccaAAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCT                         <  2:2775149/97‑1 (MQ=1)                                                                               gcC.AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGGTG                        >  1:2480414/3‑101 (MQ=11)                                                                               gcC.AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTG                        >  2:2308210/3‑101 (MQ=11)                                                                                cC.AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTTCTTTTTTGGCTGC                       >  2:1091868/2‑101 (MQ=2)                                                                                cC.AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGC                       <  1:1680272/100‑1 (MQ=11)                                                                                cC.AAGAGGGGGCAGCCCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGC                       <  2:184474/100‑1 (MQ=11)                                                                                 C.AAGGGGGGGCGGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCG                      <  2:464377/101‑1 (MQ=14)                                                                                   AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGGTGCcg                     >  1:3330166/1‑99 (MQ=1)                                                                                   AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTTCGG                     >  2:1539855/1‑101 (MQ=1)                                                                                   AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGG                     <  2:2731751/101‑1 (MQ=1)                                                                                   AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGG                     >  2:1036040/1‑101 (MQ=1)                                                                                   AAGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGG                     >  1:411133/1‑101 (MQ=1)                                                                                    AGAGGGGGCGGCCCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGC                    <  1:4276275/101‑1 (MQ=17)                                                                                    AGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGC                    >  1:2475465/1‑101 (MQ=1)                                                                                    AGAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGC                    >  2:2159973/1‑101 (MQ=1)                                                                                     ggGGGGGCCGCCCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCG                   <  1:947711/99‑1 (MQ=0)                                                                                     ggGGGGCCAGCCCCCCCGGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCG                   <  2:3804767/99‑1 (MQ=0)                                                                                     GAGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCG                   >  2:2213723/1‑101 (MQ=1)                                                                                      gGGGGACAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGC                  <  2:2784065/100‑1 (MQ=1)                                                                                      AGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTTGCTGCGGCGC                  >  2:1935756/1‑101 (MQ=1)                                                                                      AGGGGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGC                  >  2:3345049/1‑101 (MQ=1)                                                                                       ggccccccccCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCA                 <  2:3475794/91‑1 (MQ=2)                                                                                       GGGGGCCGCCCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCA                 <  2:1373577/101‑1 (MQ=0)                                                                                       GGGGGCCGCCCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCA                 <  2:3902749/101‑1 (MQ=0)                                                                                         ggccgcccCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGC               <  1:2221309/93‑1 (MQ=9)                                                                                         gcgcggccCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGC               <  2:3422221/93‑1 (MQ=14)                                                                                         GGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGGGCAGC               >  2:3519532/1‑101 (MQ=1)                                                                                         GGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGC               >  1:2444409/1‑101 (MQ=1)                                                                                         GGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGC               <  1:2008294/101‑1 (MQ=1)                                                                                         GGGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCCTGTTTGGCTGGGGCGCCGC               >  1:2748334/1‑101 (MQ=0)                                                                                          gccgcccCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGCG              <  2:2691244/94‑1 (MQ=2)                                                                                          GGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGGGGGGCAGCG              >  2:1875840/1‑101 (MQ=0)                                                                                          GGCAGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGCG              >  1:1727956/1‑101 (MQ=1)                                                                                            gccccCCCCCCCCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGCGGC            <  2:3924212/96‑1 (MQ=2)                                                                                             gcccCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACCCCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGCGGCT           <  1:3488826/97‑1 (MQ=2)                                                                                             AGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGCGGCT           >  2:1564365/1‑101 (MQ=1)                                                                                             AGCGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGCGGCT           >  2:1376722/1‑101 (MQ=1)                                                                                              gccCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGCGGCTA          <  1:2707709/98‑1 (MQ=11)                                                                                               CGCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGCGGCTAA         <  1:638728/101‑1 (MQ=1)                                                                                               CGCCCCCGGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGCGGCTAA         <  1:4318304/101‑1 (MQ=1)                                                                                                GCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGGGGCGCAGCGGCTAAT        >  2:1110383/1‑101 (MQ=1)                                                                                                GCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGCGGCTAAT        >  1:4130125/1‑101 (MQ=1)                                                                                                GCCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGCGGCTAAT        >  2:4209195/1‑101 (MQ=1)                                                                                                 CCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGCGGCTAATC       >  1:1446566/1‑101 (MQ=1)                                                                                                 CCCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGCGGCTAATC       <  2:732125/101‑1 (MQ=1)                                                                                                                                                                                                            TTGGAGCAAGATGAAAGCACGATCTGCGGTTTTCATTTATCTTGCTTCAAATATCCCGGGGGGTGAATTGGCCGAGAGGGC.AAGAGGGGGCAGCGCCCCCT....................................................................................................  >  NC_014034/1478547‑1478647 .................................................................................................CCCCTGCCCCGCCGGATCCGGGGCGGACCGGGTCCGCAAGGGCACACCTGCGCGCCAAGTGCAGCGGCTTGCTTGTTTGGCTGCGGCGCAGCGGCTAATCAGACA  >  NC_014034/2600957‑2601056 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 27 ≤  ATCG  < 34 ≤  ATCG  < 41 ≤  ATCG