New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_014034 1253895 =93 (0.210)71 (0.160) 11/196 34.0 0.18 intergenic (+53/+38) RCAP_rcc01181/hisH hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
?NC_014034 = 2714739 546 (1.190)intergenic (‑68/+11) dht/amaB dihydropyrimidinase/N‑carbamoyl‑L‑amino acid amidohydrolase
Rejected: Position hash score below cutoff.

CCCGGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCG....................................................................................................  <  NC_014034/1253996‑1253895
.....................................................................................................CGGGGGCGCAGCCCCCGGACCCCCGAGATATTTAGGGCAAGATGAAAGCACGCGCTTGCAGGGAGTGCACATGACCACAGTCATCAGGAACGGAACCATCGT  <  NC_014034/2714739‑2714640
                                                                                                                                                                                                           
  CGGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGG                                                                                                     >  1:6296051/1‑101 (MQ=1)
  CGGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGG                                                                                                     >  2:3856785/1‑101 (MQ=1)
   GGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGG                                                                                                    >  1:142184/1‑101 (MQ=1)
   GGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGG                                                                                                    <  2:5707086/101‑1 (MQ=1)
   GGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCCGG                                                                                                    >  1:7643114/1‑101 (MQ=1)
   GGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCCGG                                                                                                    >  1:5053519/1‑101 (MQ=1)
    GAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGCGGCGACCC.GGCGGGG                                                                                                   >  2:8341546/1‑101 (MQ=1)
     AGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGG                                                                                                  >  2:6121955/1‑101 (MQ=1)
      GAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCCGGGCGGGGG                                                                                                  >  1:1877496/1‑101 (MQ=11)
      GAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCCGGGGg                                                                                                 >  2:280372/1‑100 (MQ=1)
       AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGcatg                                                                                                <  2:4331217/101‑5 (MQ=1)
       AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGgg                                                                                                >  2:475652/1‑99 (MQ=1)
       AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGgg                                                                                                >  1:2702243/1‑99 (MQ=1)
       AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGgc                                                                                                >  2:6545792/1‑99 (MQ=1)
       AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCt                                                                                                <  2:7017969/101‑2 (MQ=1)
       AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCt                                                                                                <  2:7903739/101‑2 (MQ=1)
       AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCt                                                                                                >  2:4816373/1‑100 (MQ=1)
       AAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCc                                                                                                >  2:4986313/1‑100 (MQ=1)
        AATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCTGGGGCGC                                                                                               >  2:1235628/1‑101 (MQ=1)
        AATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGggg                                                                                               >  2:6031137/1‑98 (MQ=1)
        AATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGgcc                                                                                               >  1:8770299/1‑98 (MQ=1)
         ATCGCAGTGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCtcc                                                                                              <  1:7077297/101‑4 (MQ=1)
         ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGgtcc                                                                                              >  2:3454441/1‑97 (MQ=1)
         ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGgggc                                                                                              >  2:137421/1‑97 (MQ=1)
         ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGGGCc                                                                                              >  1:9083315/1‑100 (MQ=1)
         ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCtcc                                                                                              <  1:6252050/101‑4 (MQ=1)
         ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCtcc                                                                                              <  2:555277/101‑4 (MQ=1)
         ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCtcc                                                                                              <  2:8340626/101‑4 (MQ=1)
         ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCtcc                                                                                              <  2:4784073/101‑4 (MQ=1)
         ATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCtcc                                                                                              <  1:2593928/101‑4 (MQ=1)
           CGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCCGGGGGGCgcg                                                                                            >  2:3327251/1‑98 (MQ=0)
            GCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGgtccgcc                                                                                           >  2:8736253/1‑94 (MQ=1)
            GCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCC                                                                                           <  2:1070970/101‑1 (MQ=1)
            GCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCC                                                                                           <  2:5675098/101‑1 (MQ=1)
             CAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGgtcccccc                                                                                          >  1:5956682/1‑93 (MQ=0)
             CAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCC                                                                                          <  1:2103702/101‑1 (MQ=1)
              AGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGGGGGGGGGCCGCCCC                                                                                         >  2:7607535/1‑101 (MQ=0)
              AGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCC                                                                                         <  2:5197046/101‑1 (MQ=1)
              AGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCC                                                                                         >  2:7626893/1‑101 (MQ=1)
               GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGTCCC.GGCGGGGGCTCCGCCCCC                                                                                        <  1:9189978/101‑1 (MQ=1)
               GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCC                                                                                        <  1:6122192/101‑1 (MQ=1)
               GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCC                                                                                        <  2:5925086/101‑1 (MQ=1)
               GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCC                                                                                        <  2:3660782/101‑1 (MQ=1)
               GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCC                                                                                        <  2:8165954/101‑1 (MQ=1)
               GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCC                                                                                        <  1:2750882/101‑1 (MQ=1)
               GCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCC                                                                                        <  1:8249661/101‑1 (MQ=1)
                CGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCtcccgccccc                                                                                       >  2:8283417/1‑91 (MQ=0)
                CGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCG                                                                                       <  2:2499002/101‑1 (MQ=1)
                CGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCG                                                                                       <  1:3149522/101‑1 (MQ=1)
                CGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCG                                                                                       <  1:8556298/101‑1 (MQ=1)
                 GCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGGTCCGCCCCCGc                                                                                      >  2:3658425/1‑100 (MQ=11)
                 GCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGGGCCGCCCCCcc                                                                                      >  2:1815223/1‑99 (MQ=2)
                 GCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGc                                                                                      <  1:6582211/101‑2 (MQ=11)
                  CACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGGGCCGCCCCCccc                                                                                     >  1:1088963/1‑98 (MQ=2)
                   cCCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCAC                                                                                    <  2:400752/100‑1 (MQ=17)
                   ACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCAC                                                                                    <  1:3938966/101‑1 (MQ=32)
                    CCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACC                                                                                   <  1:779195/101‑1 (MQ=32)
                     CGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCC                                                                                  <  1:5883511/101‑1 (MQ=32)
                      GGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCC                                                                                 <  1:8592566/101‑1 (MQ=32)
                      GGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCC                                                                                 <  2:3092275/101‑1 (MQ=32)
                      GGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCC                                                                                 <  2:3206749/101‑1 (MQ=32)
                       GGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCC                                                                                <  2:1461199/101‑1 (MQ=32)
                       GGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCC                                                                                <  1:8775277/101‑1 (MQ=32)
                       GGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCC                                                                                <  1:6102354/101‑1 (MQ=32)
                        GCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCCG                                                                               <  1:454361/101‑1 (MQ=32)
                        GCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCCG                                                                               <  2:9083840/101‑1 (MQ=32)
                          TGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCCGAG                                                                             <  2:7387165/101‑1 (MQ=33)
                          TGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCCGAG                                                                             <  1:2269673/101‑1 (MQ=33)
                            CGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCCGAGgt                                                                           <  1:9036079/101‑3 (MQ=32)
                            CGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCCGAGgt                                                                           <  2:2238237/101‑3 (MQ=32)
                            CGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCGGGGGCTCCGCCCCCGCACCCCCGAGgt                                                                           <  1:3083312/101‑3 (MQ=32)
                                                                                                                                                                                                           
CCCGGAGAAATCGCAGCGCACCGGGCTGCGGATCATCTCGAATTTCCTGAACTGGAAGCCGTGAGAGGATTTCGCCTCGGCTTTCGCCGAGGCGACCC.GGCG....................................................................................................  <  NC_014034/1253996‑1253895
.....................................................................................................CGGGGGCGCAGCCCCCGGACCCCCGAGATATTTAGGGCAAGATGAAAGCACGCGCTTGCAGGGAGTGCACATGACCACAGTCATCAGGAACGGAACCATCGT  <  NC_014034/2714739‑2714640

Base quality scores:  ATCG  < 3 ≤  ATCG  < 23 ≤  ATCG  < 31 ≤  ATCG  < 34 ≤  ATCG  < 40 ≤  ATCG