New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	300660 =	227 (1.090)	56 (0.270)	13/184	25.0	0.32	intergenic (+13/+131)	RCAP_rcc00263/RCAP_rcc00264	winged helix family two component transcriptional regulator/hypothetical protein
	?	NC_014034	1608059 =	15 (0.070)					intergenic (+329/‑18)	RCAP_rcc01484/murD	hypothetical protein/UDP‑N‑acetylmuramoylalanine‑‑D‑glutamate ligase
Rejected: Position hash score below cutoff.

AAGCGGACTCCCCCCGGGATATTTTCACCAAGGTGAAAGCAGATCCCGGGGTGCCCTTTCACCTTGGTGCAAATATCCCACGGGGGCGCGGGGGTGTGAAACCCCCGC...................................................................................................  <  NC_014034/300767‑300660 ....................................................................................................ACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGTCTGGCCACGGCGGCGGCA  >  NC_014034/1608059‑1608157                                                                                                                                                                                                                                                                              tcttgcctCAAATATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTC                                               >  2:3303958/9‑101 (MQ=39)                                                              tcttgcctCAAATATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTC                                               <  2:4320596/93‑1 (MQ=39)                                                               cttgcctCAAATATCCCNCGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCG                                              <  2:2213227/94‑1 (MQ=39)                                                               cttgcctCAAATATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCG                                              >  2:3740700/8‑101 (MQ=39)                                                                 tgcctCAAATATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCG                                            >  2:2316397/6‑101 (MQ=38)                                                                 tgcctCAAATATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCG                                            >  2:769553/6‑101 (MQ=38)                                                                   cctCAAATATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGT                                          >  2:2118075/4‑101 (MQ=35)                                                                    ctCAAATATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGGTTACGGAGGTCGCAGATGAGACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTG                                         >  1:3807135/3‑101 (MQ=19)                                                                    ctCAAATATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTG                                         >  1:1674548/3‑101 (MQ=34)                                                                    ctCAAATATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTG                                         >  2:3366918/3‑101 (MQ=34)                                                                    ctCAAATATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTG                                         <  1:2155043/99‑1 (MQ=34)                                                                        AATATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGG                                     >  1:3468806/1‑101 (MQ=32)                                                                        AATATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGG                                     <  1:2587108/101‑1 (MQ=32)                                                                        AATATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGG                                     >  1:1741914/1‑101 (MQ=32)                                                                         ATATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGG                                    >  1:3687742/1‑101 (MQ=32)                                                                         ATATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGG                                    >  2:1502492/1‑101 (MQ=32)                                                                          TATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGG                                   >  1:3295529/1‑101 (MQ=32)                                                                           ATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGC                                  >  1:3574344/1‑101 (MQ=32)                                                                           ATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGC                                  >  2:3955838/1‑101 (MQ=32)                                                                           ATCCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGC                                  >  2:3630334/1‑101 (MQ=32)                                                                            TCCCGCGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCT                                 <  1:3544309/101‑1 (MQ=14)                                                                             CCCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCAGGGGatg                                <  2:2250326/101‑4 (MQ=2)                                                                              CCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCG                               >  2:4439006/1‑101 (MQ=1)                                                                              CCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCG                               >  1:2650944/1‑101 (MQ=1)                                                                              CCACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCG                               <  2:1535502/101‑1 (MQ=1)                                                                                ACGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGG                             <  2:3118282/101‑1 (MQ=1)                                                                                 CGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGC                            >  2:3170388/1‑101 (MQ=1)                                                                                 CGGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCGCGatc                            <  2:2336477/101‑4 (MQ=0)                                                                                  GGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCG                           >  2:1908984/1‑101 (MQ=1)                                                                                  GGGGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCG                           >  2:329141/1‑101 (MQ=1)                                                                                    GGGTGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCT                         >  1:2050041/1‑101 (MQ=1)                                                                                     ggtGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTTCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTC                        <  2:1703473/98‑1 (MQ=1)                                                                                     ggtGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTC                        >  1:515676/4‑101 (MQ=1)                                                                                       tGCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGG                      <  1:1709026/100‑1 (MQ=1)                                                                                        GCGGGGGTGTGAACCCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGG                     <  2:3919940/101‑1 (MQ=1)                                                                                        GCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGCTGCTGGGGCTCGGGCGCTCGGG                     >  2:755784/1‑101 (MQ=1)                                                                                        GCGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTACGCGCGTCGCGGTGCTGGGGATCGGGCGCTCGGG                     >  1:3828054/1‑101 (MQ=0)                                                                                         gGGGGGTGTGAACCCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGT                    <  1:397238/100‑1 (MQ=11)                                                                                         CGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGg                    >  1:4362308/1‑100 (MQ=1)                                                                                         CGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGT                    <  2:869692/101‑1 (MQ=1)                                                                                         CGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGT                    >  2:2848497/1‑101 (MQ=1)                                                                                         CGGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGT                    >  1:2337936/1‑101 (MQ=1)                                                                                          GGGGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGgc                   >  2:1623668/1‑99 (MQ=1)                                                                                            GGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGTCTG                 >  2:3049709/1‑101 (MQ=1)                                                                                            GGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGTCTG                 <  2:2855529/101‑1 (MQ=1)                                                                                            GGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGTCTG                 <  2:3197532/101‑1 (MQ=1)                                                                                            GGGTGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCCGGCGCTCGGGgccg                 >  2:1716454/1‑97 (MQ=0)                                                                                            GGGTGAGAACCCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGTCTG                 <  1:3818337/101‑1 (MQ=0)                                                                                               gGTGAACCCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGTCTGGCC              <  1:3956094/100‑1 (MQ=1)                                                                                               TGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGTCTGGCC              >  1:980875/1‑101 (MQ=1)                                                                                               TGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGTCTGGCC              >  1:3113801/1‑101 (MQ=1)                                                                                               TGTGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGTCTGGCC              >  1:2152608/1‑101 (MQ=1)                                                                                                 TGAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCTGGCGCTCGGGTCTGGCCAC            >  1:2527691/1‑101 (MQ=1)                                                                                                  GAAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGTCTGGCCACG           <  1:2921619/101‑1 (MQ=1)                                                                                                   AAACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGTCTGGCCACGG          >  2:2170299/1‑101 (MQ=1)                                                                                                    AACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGTCTGGCCACGGC         <  1:4366978/101‑1 (MQ=1)                                                                                                                                                                                                                 AAGCGGACTCCCCCCGGGATATTTTCACCAAGGTGAAAGCAGATCCCGGGGTGCCCTTTCACCTTGGTGCAAATATCCCACGGGGGCGCGGGGGTGTGAAACCCCCGC...................................................................................................  <  NC_014034/300767‑300660 ....................................................................................................ACCCCCGCAGCTTACGGAGGTCGCAGATGATACCGGTTCAGGGATATGAGGGTGCGCGCGTCGCGGTGCTGGGGCTCGGGCGCTCGGGTCTGGCCACGGCGGCGGCA  >  NC_014034/1608059‑1608157 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 29 ≤  ATCG  < 34 ≤  ATCG  < 40 ≤  ATCG