New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	925895 =	354 (1.010)	80 (0.230)	30/196	21.7	0.27	intergenic (+148/+26)	RCAP_rcc00838/glcB	DnaJ domain‑containing protein/malate synthase
	?	NC_014034	1255906 =	71 (0.200)					intergenic (+76/+166)	RCAP_rcc01184/RCAP_rcc01185	CsbD family protein/methyl‑accepting chemotaxis sensory transducer
Rejected: Position hash score below cutoff.

GGATCCAGTCCTCGGGCTATACCGAGCCGGTGCTGCACCAGCGCCGGGCGCAGGTGAAGGCCGCCAAAGCATAAGAAA.GGGGGGGCGCTGCCCCCCGTCC....................................................................................................  <  NC_014034/925994‑925895 ....................................................................................................CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGGGAACTTCCCGA  >  NC_014034/1255906‑1256005                                                                                                                                                                                                             ATCCAGTCCTCGGGCTATACCGAGCCGGTGCTGCACCAGCGCCGGGCGCAGGTGAAGGCCGCCAAAGCATAAGAAAGGGGGGGGCGCTGCCCCCCGGCCCC                                                                                                    >  1:5761894/1‑101 (MQ=255)                                                                        ccgaagA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAA                             <  2:103447/95‑1 (MQ=255)                                                                         cgaagA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAA                            >  1:2566161/6‑101 (MQ=255)                                                                         cgaagA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAA                            >  1:2582643/6‑101 (MQ=255)                                                                         cgaagA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAA                            >  1:4157429/6‑101 (MQ=255)                                                                          gaagA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAAT                           >  2:6491029/5‑101 (MQ=255)                                                                          gaagA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAAT                           <  2:3145581/97‑1 (MQ=255)                                                                          gaagA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAAT                           <  1:2022662/97‑1 (MQ=255)                                                                          gaagA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAAT                           <  1:6998795/97‑1 (MQ=255)                                                                          gaagA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAAT                           >  1:6059032/5‑101 (MQ=255)                                                                           aagA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATA                          >  2:6796217/4‑101 (MQ=255)                                                                           aagA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATA                          >  1:927931/4‑101 (MQ=255)                                                                           aagA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATA                          >  1:4223528/4‑101 (MQ=255)                                                                           aagA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATA                          <  2:5439145/98‑1 (MQ=255)                                                                           aagA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCCTGGGCCAAATA                          >  2:4835571/4‑101 (MQ=255)                                                                            agA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATAT                         <  2:1829418/99‑1 (MQ=255)                                                                            agA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATAT                         <  2:281988/99‑1 (MQ=255)                                                                            agA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATAT                         >  2:6473495/3‑101 (MQ=255)                                                                            agA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATAT                         >  1:6620590/3‑101 (MQ=255)                                                                            agA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATAT                         >  1:6075578/3‑101 (MQ=255)                                                                            agA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATAT                         <  1:2234091/99‑1 (MQ=255)                                                                            agA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATAT                         >  2:4953245/3‑101 (MQ=255)                                                                            agA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATAT                         <  1:378941/99‑1 (MQ=255)                                                                             gA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATC                        <  2:187429/100‑1 (MQ=255)                                                                             gA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATC                        >  1:1211366/2‑101 (MQ=255)                                                                             gA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATC                        <  2:5138369/100‑1 (MQ=255)                                                                             gA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATC                        <  1:2591684/100‑1 (MQ=255)                                                                             gA.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATC                        >  1:840265/2‑101 (MQ=255)                                                                              A.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCC                       >  2:1715596/1‑101 (MQ=255)                                                                              A.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCC                       <  1:809475/101‑1 (MQ=255)                                                                              A.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCC                       >  2:6473186/1‑101 (MQ=255)                                                                              A.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCC                       >  1:3002286/1‑101 (MQ=255)                                                                              A.GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCC                       >  2:4361048/1‑101 (MQ=255)                                                                                GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCC                      <  2:5957163/101‑1 (MQ=255)                                                                                GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCC                      >  2:5368614/1‑101 (MQ=255)                                                                                GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCC                      <  2:1443274/101‑1 (MQ=255)                                                                                GGGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCC                      >  2:1491172/1‑101 (MQ=255)                                                                                 GGGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCG                     <  2:3891231/101‑1 (MQ=255)                                                                                  GGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGG                    >  2:1027985/1‑101 (MQ=255)                                                                                  GGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGG                    >  1:4982854/1‑101 (MQ=255)                                                                                  GGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGG                    <  2:1103161/101‑1 (MQ=255)                                                                                  GGGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGG                    >  1:3231667/1‑101 (MQ=255)                                                                                   GGGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGG                   >  1:2103299/1‑101 (MQ=255)                                                                                    GGGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGG                  >  1:2358870/1‑101 (MQ=255)                                                                                     GGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGG                 <  2:2903755/101‑1 (MQ=255)                                                                                     GGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGG                 >  2:4941896/1‑101 (MQ=255)                                                                                     GGCGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGG                 >  1:97376/1‑101 (MQ=255)                                                                                       CGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGG               >  1:3160958/1‑101 (MQ=255)                                                                                       CGCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGG               >  1:3629921/1‑101 (MQ=255)                                                                                        GCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGG              >  2:5416077/1‑101 (MQ=255)                                                                                        GCTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGG              <  1:1848429/101‑1 (MQ=255)                                                                                         CTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGG             >  2:3065435/1‑101 (MQ=255)                                                                                         CTGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGG             >  1:4940416/1‑101 (MQ=255)                                                                                          TGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGGa            <  2:1976167/101‑2 (MQ=255)                                                                                          TGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGGG            >  1:5408846/1‑101 (MQ=255)                                                                                          TGCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGGG            <  1:3497247/101‑1 (MQ=255)                                                                                           GCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAGCCCGGGGCGCGGCTTTCACCTGGGGCCAAATATCCCGGGGGGGGGGA           <  1:4266994/101‑1 (MQ=255)                                                                                           GCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGGGA           <  2:1856897/101‑1 (MQ=255)                                                                                           GCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGGGA           >  2:2474131/1‑101 (MQ=255)                                                                                           GCCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGGGA           <  2:1168530/101‑1 (MQ=255)                                                                                            CCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCCCCTTGGGCCAAATATCCCGGGGGGGGGGAA          <  2:5911733/101‑1 (MQ=255)                                                                                            CCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGGGAA          >  1:2207803/1‑101 (MQ=255)                                                                                            CCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGGGAA          >  1:7000287/1‑101 (MQ=255)                                                                                            CCCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCGTTCACCTTGGGCCAAATATCCCGGGGGGGGGGAA          >  2:5904158/1‑101 (MQ=255)                                                                                             CCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGGGAct         >  1:2014252/1‑99 (MQ=255)                                                                                             CCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGGGAAC         <  1:1660491/101‑1 (MQ=255)                                                                                             CCCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGGGAAC         >  1:1102310/1‑101 (MQ=255)                                                                                              CCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCCCCTTGGGCCAAATATCCCGGGGGGGGGGAACT        <  1:5960958/101‑1 (MQ=255)                                                                                              CCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCCCCTTGGGCCAAATATCCCGGGGGGGGGGAACT        <  2:1757449/101‑1 (MQ=255)                                                                                              CCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGGGAACT        >  2:625351/1‑101 (MQ=255)                                                                                              CCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGGGAACT        <  1:4849002/101‑1 (MQ=255)                                                                                              CCCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGGGAACT        <  2:1304707/101‑1 (MQ=255)                                                                                               CCCGT.CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGGGAACTT       >  2:5414617/1‑101 (MQ=255)                                                                                                                                                                                                           GGATCCAGTCCTCGGGCTATACCGAGCCGGTGCTGCACCAGCGCCGGGCGCAGGTGAAGGCCGCCAAAGCATAAGAAA.GGGGGGGCGCTGCCCCCCGTCC....................................................................................................  <  NC_014034/925994‑925895 ....................................................................................................CCCTGCGGGACTCCCCCCGGGATATTTCCGCCAAGGGGAAATGAACCCGGGGCGCGGCTTTCACCTTGGGCCAAATATCCCGGGGGGGGGGAACTTCCCGA  >  NC_014034/1255906‑1256005 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 29 ≤  ATCG  < 34 ≤  ATCG  < 40 ≤  ATCG