New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2887322 =	47 (0.870)	3 (0.060)	3/468	NT	7.0%	intergenic (‑105/‑30)	ygcB/sokX	Cascade complex anti‑viral R‑loop helicase‑annealase Cas3/sok‑related sRNA, function unknown
	?	NC_000913	2887733 =	34 (0.650)					coding (578/735 nt)	cysH	phosphoadenosine phosphosulfate reductase, PAPS reductase, thioredoxin dependent

CGAGCAGCATTCCTGATTTTAAACGTGAACGCCGCGGGAAGAATTATCAGGTATAGAATGGCGTCGGGTGCTTGAGGCTGTCTGGCGTTAAGCATTCGCGAGGTTCCAGATGGACAAAAGCCCCAGGCGATATTTCTATCAACCTGAGGCCAGCGTTCGAACCCAAACAATTCGAATGTTAGTCTCTTCTTTGCA‑GG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2887518‑2887322 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tttgca‑ggTACTGATAAATAGTTCGGTTA‑TCCCAGTCGATAATCGGCAGCACTTTAAATACGCCACGCTGAATTGCCAGCACCGGTAAATTGGCACGACTGCCGGATTGTTCACGGCGCAGGCCAGCAAACCAGGTTTGCGCATTCAGTTCTTTCAGAGCCCGGTTCATCGGTTCGACTTTGTTGATGTCATTGTACTTTTCAATGCCTTCAACGCCCTGCTCCCACAGTTTTCCGTAGCGTGCTTCCTGCCAGGCTGCGCTTTCGGTAGCACGGTA  >  NC_000913/2887733‑2888001                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CGAGCAGCATTCCTGATTTTAAACGTGAACGCCGCGGGAAGAATTATCAGGTATAGAATGGCGTCGGGTGCTTGAGGCTGTCTGGCGTTAAGCATTCGCGAGGTTCCAGATGGACAAAAGCCCCAGGCGATATTTCTATCAACCTGAGGCCAGCGTTCGAACCCAAACAATTCGAATGTTAGTCTCTTCTTTGCA‑GGTACTGATAAATAGTTCGGTTA‑TCCCAGTCGATAATCGGCAGCACTTTAAATA                                                                                                                                                                                                                           >  2:46318/1‑249     CAGCATTCCTGATTTTAAACGTGAACGCCGCGGGAAGAATTATCAGGTATAGAATGGCGTCGGGTGCTTGAGGCTGTCTGGCGTTAAGCATTCGCGAGGTTCCAGATGGACAAAAGCCCCAGGCGATATTTCTATCAACCTGAGGCCAGCGTTCGAACCCAAACAATTCGAATGTTAGTCTCTTCTTTGCA‑GGTACTGATAAATAGTTCGGTTA‑TCCCAGTCGATAATCGGCAGCACTTTAAATACGCC                                                                                                                                                                                                                       <  1:46318/249‑1                                                              CGTCGGGTGCTTGAGGCTGTCTGGCGTTAAGCATTCGCGAGGTTCCAGATGGACAAAAGCCCCAGGCGATATTTCTATCAACCTGAGGCCAGCGTTCGAACCCAAACAATTCGAATGTTAGTCTCTTCTTTG                                                                                                                                                                                                                                                                                     >  1:85973/1‑132                                                                  GGGTGCTTGAGGCTGTCTGGCGTTAAGCATTCGCGAGGTTCCAGATGGACAAAAGCCCCAGGCGATATTTCTATCAACCTGAGGCCAGCGTTCGAACCCAAACAATTCGAATGTTAGTCTCTTCTTTGCA‑GG                                                                                                                                                                                                                                                                                <  2:85972/132‑1                                                                                          AAGCATTCGCGGGGTTCCAGATTGACAAAAGCCCCAGGCGATATTTCTATCAACCTGAGGCCAGCGTTCTAACCCAAACAATTCGAATGTTAGTCTCTTCTTTGCAGGGAAGCAAGACATGTGTATATCACTGTAATTCGATAATCGGCAGCACTTTAAATACGCCACTCTGAATTGCCAGCACCGGTAAATTGGCACGACTGCCGGATTGTTCACGGCGCAGGCCAGCAAACCAGGTTTGCGCATTCAGTTCTTTCAGAGCCCGGTTCATCGG                                                                                                           <  1:413433/274‑1                                                                                                                            CAGGCGATATTTCTATCAACCTGAGGCCAGCGTTCGAACCCAAACAATTCGAATGTTAGTCTCTTCTTTGCA‑GG                                                                                                                                                                                                                                                                                >  1:224296/1‑74                                                                                                                                                                                                TGCA‑GGTACTGATAAATAGTTCGGTTA‑TCCCAGTCGATAATCGGCAGCACTTTAAATACGCCACGCTGAATTGCCAGCACCGGTAAATTGGCACGACTGCCGGATTGTTCACGGCGCAGGCCAGCAAACCAGGTTTGCGCATTCAGTTCTTTCAGAGCCCGGTTCATCGGTTCGACTTTGTTGATGTCATTGTACTTTTCAATGCCTTCAACGCCCTGCTCCCACAGTTTTCCGTAGCGTGCTTCCTGCCAGGCTGCGCTTTCGGTAGCACGGTA  <  1:282368/275‑1                                                                                                                                                                                                TGCA‑GGTACTGATAAATAGTTCGGTTA‑TCCCAGTCGATAATCGGCAGCACTTTAAATACGCCACGCTGAATTGCCAGCACCGGTAAATTGGCACGACTGCCGGATTGTTCACGGCGCAGGCCAGCAAACCAGGTTTGCGCATTCAGTTCTTTCAGACCCCGGTTCATCGGTTCGACTTTGTTGATGTCATTGTACTTTTCAATGCCTTCAACGCCCTGCTCCCACAGTTTTCCGTAGCGTGCTTCCTGCCAGGCTGCGCTTTCGGTAGCACGGTA  <  2:452589/275‑1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CGAGCAGCATTCCTGATTTTAAACGTGAACGCCGCGGGAAGAATTATCAGGTATAGAATGGCGTCGGGTGCTTGAGGCTGTCTGGCGTTAAGCATTCGCGAGGTTCCAGATGGACAAAAGCCCCAGGCGATATTTCTATCAACCTGAGGCCAGCGTTCGAACCCAAACAATTCGAATGTTAGTCTCTTCTTTGCA‑GG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2887518‑2887322 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tttgca‑ggTACTGATAAATAGTTCGGTTA‑TCCCAGTCGATAATCGGCAGCACTTTAAATACGCCACGCTGAATTGCCAGCACCGGTAAATTGGCACGACTGCCGGATTGTTCACGGCGCAGGCCAGCAAACCAGGTTTGCGCATTCAGTTCTTTCAGAGCCCGGTTCATCGGTTCGACTTTGTTGATGTCATTGTACTTTTCAATGCCTTCAACGCCCTGCTCCCACAGTTTTCCGTAGCGTGCTTCCTGCCAGGCTGCGCTTTCGGTAGCACGGTA  >  NC_000913/2887733‑2888001

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ 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.