New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	3012400 =	NA (NA)	19 (0.140)	8/166	NT	NA	intergenic (+7/+214)	yqeA/yqeB	putative amino acid kinase/XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold
	?	NC_000913	3012426 =	NA (NA)					noncoding (26/204 nt)	RIP209 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site	RIP209 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site

TTGCGATGTTTTGTAGGACGGATAAGGCGCTCGCGCCGCATCCGGCATCAACAAAGCGCACTTACTTGACAATCTTTGGCCGGAT‑GGTATTACCCACCCGGCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3012502‑3012400 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccggccAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCACT  >  NC_000913/3012426‑3012524                                                                                                                                                                                                             TTGCGATGTTTTGTAGGACGGATAAGGCGCTCGCGCCGCATCCGGCATCAACAAAGCGCACTTACTTGACAATCTTTGGCCGGAT‑GGTATTACCCACCCG                                                                                                        <  2:2256206/100‑1  TGCGATGTTTTGTAGGACGGATAAGGCGCTCGCGCCGCATCCGGCATCAACAAAGCGCACTTACTTGACAATCTTTGGCCGGAT‑GGTATTACCCACCCGG                                                                                                       >  2:2597519/1‑100   GCGATGTTTTGTAGGACGGATAAGGCGCTCGCGCCGCATCCGGCATCAACAAAGCGCACTTACTTGACAATCTTTGGCCGGAT‑GGTATTACCCACCCGGC                                                                                                      <  2:3306731/100‑1   GCGATGTTTTGTAGGACGGATAAGGCGCTCGCGCCGCATCCGGCATCAACAAAGCGCACTTACTTGACAATCTTTGGCCGGAT‑GGTATTACCCACCCGGC                                                                                                      <  2:1818648/100‑1   GCGATGTTTTGTAGGACGGATAAGGCGCTCGCGCCGCATCCGGCATCAACAAAGCGCACTTACTTGACAATCTTTGGCCGGAT‑GGTATTACCCACCCGGC                                                                                                      >  1:2323185/1‑100    CGATGTTTTGTAGGACGGATAAGGCGCTCGCGCCGCATCCGGCATCAACAAAGCGCACTTACTTGACAATCTTTGGCCGGAT‑GGTATTACCCACCCGGCC                                                                                                     >  2:1502582/1‑100             GTAGGACGGATAAGGCGCTCGCGCCGCATCCGGCATCAACAAAGCGCACTTACTTGACAATCTTTGGCCGGGTGGGTAATA‑CCATCCGGCCAAAGATTGT                                                                                            <  1:2179715/100‑1                                   GCCGCATCCGGCATCAACAAAGCGCACTTACTTGACAATCTTTGGCCGGAT‑GGTATTACCCACCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGAT                                                                      >  1:568973/1‑100                                                                          CTTTGGCCGGAT‑GGTATTACCCACCCGGCCAAAGATTGTCAAGTAAGTCCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACCAAA                                >  1:741338/1‑99                                                                            TTGGCCGGAT‑GGTATTACCCACCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACAT                             >  2:2918063/1‑100                                                                            TTGGCCGGAT‑GGTATTACCCACCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACAT                             >  1:1675477/1‑100                                                                             TGGCCGGAT‑GGTATTACCCACCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATC                            >  2:1576497/1‑100                                                                              GGCCGGAT‑GGTATTACCCACCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCG                           >  1:1397473/1‑100                                                                              GGCCGGAT‑GGTATTACCCACCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCG                           >  1:1070143/1‑100                                                                              GGCCGGAT‑GGTATTACCCACCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATC                            >  1:2000315/1‑99                                                                               GCCGGAT‑GGTATTACCCACCCGGCCAAAGATTGTCTAGTAGGTGCGCTTTGTTGCTGCCGGATGCGGCGCGAGCTCCTTATCCGTCCTACAAAACACCGC                          >  2:3853549/1‑100                                                                               GCCGGAT‑GGTATTACCCACCCGGCCAAAGATTGTCAAGTGAGTGCACTTTGTTGATGCCGGATGCGGCGCGAGCGCCGTATCCGTCCTACACAACATCGC                          >  2:2960920/1‑100                                                                               GCCGGAT‑GGTATTACCCACCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGC                          >  1:3102429/1‑100                                                                               GCCGGAT‑GGTATTACCCACCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGC                          >  2:673799/1‑100                                                                               GCCGGAT‑GGTATTACCCACCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGC                          >  1:4135464/1‑100                                                                               GCCGGAT‑GGTATTACCCACCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGC                          >  1:2306698/1‑100                                                                               GCCGGAT‑GGTATTACCCACCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGC                          >  2:2111547/1‑100                                                                               GCCGGAT‑GGTATTACCCACCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGC                          >  1:1803029/1‑100                                                                               GCCGGAG‑GGTATGACCCACCCGGCCAAAGATTGTCAAGTAAGTGCGCTCTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCGGTCCTACAAAACTTCG                           >  2:3725201/1‑99                                                                                          ATTACCCACCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATA                >  2:985823/1‑100                                                                                                    CGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATG      <  1:2490134/100‑1                                                                                                     GGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGC     >  1:3940248/1‑100                                                                                                     GGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGC     <  2:3711090/100‑1                                                                                                     GGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGC     >  1:1863165/1‑100                                                                                                     GGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGC     >  2:176175/1‑100                                                                                                     GGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGC     <  1:4112115/100‑1                                                                                                      GCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCA    <  2:691788/100‑1                                                                                                       CCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCAC   >  1:1492657/1‑100                                                                                                       CCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCAC   >  2:2456903/1‑100                                                                                                       CCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCAC   >  2:60186/1‑100                                                                                                       CCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCAC   <  2:807479/100‑1                                                                                                       CCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCAC   >  1:3958182/1‑100                                                                                                        CAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCACT  >  1:1723819/1‑100                                                                                                        CAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCACT  >  1:244236/1‑100                                                                                                                                                                                                             TTGCGATGTTTTGTAGGACGGATAAGGCGCTCGCGCCGCATCCGGCATCAACAAAGCGCACTTACTTGACAATCTTTGGCCGGAT‑GGTATTACCCACCCGGCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3012502‑3012400 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccggccAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCACT  >  NC_000913/3012426‑3012524

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.