New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_007779	571584 =	246 (1.370)	28 (0.160)	25/410	NT	10.2%	intergenic (+110/‑7)	Y75_RS02805/Y75_RS23245	helix‑turn‑helix transcriptional regulator/hypothetical protein
	?	NC_007779	= 1106952	NA (NA)					intergenic (‑46/‑39)	Y75_RS05455/Y75_RS05465	IS3‑like element IS2 family transposase/hypothetical protein

TAAGCACCATGCGAAAGCATTTGCCCTCCTCCAGATAAGGCTGGATCTGCCGACCGATAGCGGTGAAGTTGCCGCGATGTAATTTGATGCCGTCTTGTGAGAGGTTCACGCTTCCCCTCCGCAGAGGTCAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_007779/571797‑571584 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATGGTGTAGCAGCCAGCCAGTTATTTCT  <  NC_007779/1106952‑1106719                                                                                                                                                                                                                                                                                                                                                                                                                                                                  TAAGCACCATGCGAAAGCATTTGCCCTCCTCCAGATAAGGCTGGATCTGCCGACCGATAGCGGTGAAGTTGCCGCGATGTAATTTGATGCCGTCTTGTGAGAGGTTCACGCTTCCCCTCCGCAGAGGTCAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGA                                                                                                                                                                                                                   <  1:1108330/239‑1   AGCACCATGCGAAAGCATTTGCCCTCCTCCAGATAAGGCTGGATCTGCCGACCGATAGCGGTGAAGTTGCCGCGATGTAATTTGATGCCGTCTTGTGAGAGGTTCACGCTTCCCCTCCGCAGAGGTCAAGCGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACA                                                                                                                                                                                                                 <  2:916789/239‑1       CCATGCGAAAGCATTTGCCCTCCTCCAGATAAGGCTGGATCTGCCGACCGATAGCGGTGAAGTTGCCGCGATGTAATTTGATGCCGTCTTGTGAGAGGTTCACGCTTCCCCTCCGCAGAGGTCAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCA                                                                                                                                                                                                             >  2:1996306/1‑239             GAAAGCATTTGCCCTCCTCCAGATAAGGCTGGATCTGCCGACCGATAGCGGTGAAGTTGCCGCGATGTAATTTGATGCCGTCTTGTGAGAGGTTCACGCTTCCCCTCCGCAGAGGTCAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATC                                                                                                                                                                                                        <  1:1128368/238‑1               AAGCATTTGCCCTCCTCCAGATAAGGCTGGATCTGCCGACCGATAGCGGTGAAGTTGCCGCGATGTAATTTGATGCCGTCTTGTGAGAGGTTCACGCTTCCCCTCCGCAGAGGTCAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCtc                                                                                                                                                                                                      <  1:1996306/238‑3                   ATTTGCCCTCATCCAGATAAGGCTGGAGCTGCCGACCGAGAGCGGTGAAGTTGCCGCGATGTAATTTGATGCCGTCTTGTGAGAGGTTCACGCTTCACCTCCGCAGAGGTCAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAA                                                                                                                                                                                                  <  2:2019414/238‑1                           tgCTCCCGATAAGGCTGGATCTGCCGACCGGTAGCGGTGAAGTTGCCGCGATGTAATTTGATGCCGTCTTGTGAGAGGTTCACGCTTCCCCTCCGCAGAGGTCAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGAT                                                                                                                                                                                         <  2:904541/237‑1                            CCTCCAGATAAGGCTGGATCTGCCGACCGATAGCGGTGAAGTTGCCGCGATGTAATTTGATGCCGTCTTGTGAGAGGTTCACGCTTCCCCTCCGCAGAGGTCAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCT                                                                                                                                                                                                                              >  2:810763/1‑201                            CCTCCAGATAAGGCTGGATCTGCCGACCGATAGCGGTGAAGTTGCCGCGATGTAATTTGATGCCGTCTTGTGAGAGGTTCACGCTTCCCCTCCGCAGAGGTCAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCT                                                                                                                                                                                                                              <  1:810763/201‑1                                         CTGGAGCTGCCGACCGGTAGCGGTGAAGTTGCCGCGATGTCATTTGATGCCGTCTTGTGAGAGGTTCACGCTTCACGTCCGCAGAGGTCAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCTCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATCCTA                                                                                                                                                                            <  2:950308/238‑1                                            GATCTGCCGACCGATAGCGGTGAAGTTGCCGCGATGTAATTTGATGCCGTCTTGTGAGAGGTTCACGCTTCCCCTCCGCAGAGGTCAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGAT                                                                                                                                                                                         <  1:1962465/222‑1                                            GATCTGCCGACCGATAGCGGTGAAGTTGCCGCGATGTAATTTGATGCCGTCTTGTGAGAGGTTCACGCTTCCCCTCCGCAGAGGTCAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGAT                                                                                                                                                                                         >  2:1962465/1‑222                                             ATCTGCCGACCGATAGCGGTGAAGTTGCCGCGATGTAATTTGATGCCGTCTTGTGAGAGGTTCACGCTTCCCCTCCGCAGAGGTCAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAAT                                                                                                                                                                                                <  1:1873557/214‑1                                             ATCTGCCGACCGATAGCGGTGAAGTTGCCGCGATGTAATTTGATGCCGTCTTGTGAGAGGTTCACGCTTCCCCTCCGCAGAGGTCAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAAT                                                                                                                                                                                                >  2:1873557/1‑214                                                          TAGCGGTGAAGTTGCCGCGATGTAATTTGATGCCGTCTTGTGAGAGGTTCACGCTTCCCCTCCGCAGAGGTCAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCAT                                                                                                                                                           <  1:1809022/238‑1                                                                                                                        CGCAGAGGTCAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAA                                                                                            >  1:289424/1‑239                                                                                                                             AGGTCAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATC                                                                                        >  2:1381520/1‑238                                                                                                                                 CAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAA                                                                                    <  1:1984417/238‑1                                                                                                                                                    ATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAG                                                                                                                                                                                                                    >  2:61898/1‑91                                                                                                                                                    ATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAG                                                                                                                                                                                                                    <  1:61898/91‑1                                                                                                                                                      TGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACC                                                              >  1:664393/1‑239                                                                                                                                                      TGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACC                                                              >  1:1332622/1‑239                                                                                                                                                                TTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACG                                                    <  1:1381520/239‑1                                                                                                                                                                     GCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCT                                                >  1:585048/1‑238                                                                                                                                                                                     AAGAGAGTTTGGATTGTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCA                                >  1:987894/1‑238                                                                                                                                                                                                    GTATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATGGTGTAGCAGCC                >  1:23867/1‑239                                                                                                                                                                                                      ATGTGCGCATAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATGGTGTAGCAGCCAG              <  2:987894/239‑1                                                                                                                                                                                                               TAAACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATGGTGTAGCAGCCAGCCAGTTATT     >  2:1584428/1‑239                                                                                                                                                                                                                  ACGTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATGGTGTAGCAGCCAGCCAGTTATTTCT  <  1:1584428/239‑1                                                                                                                                                                                                                                                                                                                                                                                                                                                                  TAAGCACCATGCGAAAGCATTTGCCCTCCTCCAGATAAGGCTGGATCTGCCGACCGATAGCGGTGAAGTTGCCGCGATGTAATTTGATGCCGTCTTGTGAGAGGTTCACGCTTCCCCTCCGCAGAGGTCAAACGCTAGATGCAAAGAATTGCAGGTGCATTTCTGCATCTGTGAAGGGAGAAGAGAGTTTGGATTGTATGTGCGCATAAACGTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_007779/571797‑571584 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATGGTGTAGCAGCCAGCCAGTTATTTCT  <  NC_007779/1106952‑1106719

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ 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.