New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	392448 =	66 (0.280)	63 (0.270)	15/192	19.8	0.66	intergenic (‑96/+47)	RCAP_rcc00363/trmD	hypothetical protein/tRNA (guanine‑N1)‑methyltransferase
	?	NC_014034	= 1253888	NA (NA)					intergenic (+46/+45)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
Rejected: Position hash score below cutoff.

AAGCTTTGACGCGGGACCGGCGGCCGGATTTGTGGGAGAAGTTCGGCAAGTGATTTCGCCTCGGCTGCGCCGAGGCGACCCGCCGGGGGCTCCGCCCCCG....................................................................................................  <  NC_014034/392547‑392448 ................................................................................................CCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCACCAT  <  NC_014034/1253888‑1253789                                                                                                                                                                                                                                                                      cggctttCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAA                                         <  1:4414247/94‑1 (MQ=32)                                                             cggctttCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAA                                         <  1:2132568/94‑1 (MQ=32)                                                             cggctttCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAA                                         <  2:2097535/94‑1 (MQ=32)                                                             cggctttCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAA                                         <  1:2636547/94‑1 (MQ=32)                                                                  ttCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGC                                    <  2:4501848/99‑1 (MQ=32)                                                                    CGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAG                                  <  1:3701578/101‑1 (MQ=32)                                                                     GCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGC                                 <  2:4467272/101‑1 (MQ=32)                                                                      CCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCC                                <  2:4402737/101‑1 (MQ=32)                                                                       CGAGGCGCCCCGGCGGGGGCTCCGCCCCCGCGCCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCG                               <  1:3658188/101‑1 (MQ=12)                                                                       CGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCG                               <  2:399269/101‑1 (MQ=32)                                                                        GAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGG                              <  2:1133117/101‑1 (MQ=32)                                                                        GAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGG                              <  2:455902/101‑1 (MQ=32)                                                                          GGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTC                            <  2:1747642/101‑1 (MQ=32)                                                                          GGCGACCCGGCGGGGGCTCCGCCCCCGCACACCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTC                            >  2:4261266/1‑101 (MQ=17)                                                                            CGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTG                          <  2:4029695/101‑1 (MQ=32)                                                                             GACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGG                         <  2:2450411/101‑1 (MQ=32)                                                                             GACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGG                         <  2:35233/101‑1 (MQ=32)                                                                              gCCCGGCGGGGGCTCCGCCCCCGCCCCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGA                        <  2:3553917/100‑1 (MQ=17)                                                                              ACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGA                        <  2:1093332/101‑1 (MQ=32)                                                                               CCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAA                       <  1:718549/101‑1 (MQ=32)                                                                               CCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAA                       <  1:2497099/101‑1 (MQ=32)                                                                                CCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAG                      <  1:3762198/101‑1 (MQ=32)                                                                                 cggccGGGGCCCCGCCCNCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGC                     <  2:2184732/96‑1 (MQ=9)                                                                                 cggCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGC                     <  2:2108552/98‑1 (MQ=32)                                                                                  ggCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGGTCGGGTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGgc                    >  2:1582293/3‑99 (MQ=9)                                                                                  ggCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCC                    <  1:3898065/99‑1 (MQ=31)                                                                                  ggCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCC                    <  2:3981516/99‑1 (MQ=31)                                                                                   gCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCG                   <  1:3450791/100‑1 (MQ=11)                                                                                   gCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCG                   <  1:3190604/100‑1 (MQ=11)                                                                                    CGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGA                  <  1:3543646/101‑1 (MQ=1)                                                                                    CGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGA                  <  2:604280/101‑1 (MQ=1)                                                                                    CGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGA                  <  2:3021901/101‑1 (MQ=1)                                                                                     GGGGGCTCCGCCCCCGCCCCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAG                 <  2:4566317/101‑1 (MQ=1)                                                                                     GGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGgg                 >  2:127770/1‑99 (MQ=1)                                                                                     GGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAG                 >  2:646284/1‑101 (MQ=1)                                                                                     GGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAG                 >  1:59153/1‑101 (MQ=1)                                                                                     GGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGGTTATTTTGCCTCGAAGGCGCCGCCGGTCTGGAAGCCGAG                 >  2:1844383/1‑101 (MQ=0)                                                                                       GGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCT               <  2:3229788/101‑1 (MQ=1)                                                                                         GCTCCGCCCCCGCGCCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTG             <  1:4503486/101‑1 (MQ=1)                                                                                          CTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGC            >  2:4609684/1‑101 (MQ=1)                                                                                          CTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGC            >  2:3848099/1‑101 (MQ=1)                                                                                           tctGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCC           <  2:1756917/98‑1 (MQ=1)                                                                                           TCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCC           >  2:4294677/1‑101 (MQ=1)                                                                                           TCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCC           >  1:1980523/1‑101 (MQ=1)                                                                                           TCCGCCCACGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCC           >  1:2024283/1‑101 (MQ=1)                                                                                           TCCCCCCCCGCACCCCCGGGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCC           <  1:2140024/101‑1 (MQ=0)                                                                                            CCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCC          >  2:506601/1‑101 (MQ=1)                                                                                            CCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCC          >  2:4992563/1‑101 (MQ=1)                                                                                            CCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCC          >  2:2232215/1‑101 (MQ=1)                                                                                            CCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCC          >  1:4628746/1‑101 (MQ=1)                                                                                            CCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCC          <  1:408207/101‑1 (MQ=1)                                                                                            CCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCC          <  1:2386431/101‑1 (MQ=1)                                                                                             CGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCA         <  1:4863853/101‑1 (MQ=1)                                                                                              GCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAG        >  1:4197647/1‑101 (MQ=1)                                                                                              GCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAG        >  1:4097759/1‑101 (MQ=1)                                                                                              GCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCCTGCCaga        >  1:1757047/1‑98 (MQ=0)                                                                                              GCCCCCGCACACCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAG        >  2:3749642/1‑101 (MQ=1)                                                                                               CCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGC       <  2:3594383/101‑1 (MQ=1)                                                                                               CCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAACGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGC       >  2:1346682/1‑101 (MQ=1)                                                                                                CCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGac      >  2:1753883/1‑99 (MQ=1)                                                                                                CCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCA      >  2:4624016/1‑101 (MQ=1)                                                                                                CCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCA      >  1:3612869/1‑101 (MQ=1)                                                                                                CCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCA      >  2:895181/1‑101 (MQ=1)                                                                                                                                                                                                          AAGCTTTGACGCGGGACCGGCGGCCGGATTTGTGGGAGAAGTTCGGCAAGTGATTTCGCCTCGGCTGCGCCGAGGCGACCCGCCGGGGGCTCCGCCCCCG....................................................................................................  <  NC_014034/392547‑392448 ................................................................................................CCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCACCAT  <  NC_014034/1253888‑1253789 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG