New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2996219 =	76 (0.770)	4 (0.040)	4/246	NT	5.0%	pseudogene (142/399 nt)	ygeO	pseudogene, orgA family, part of T3SS PAI ETT2 remnant
	?	NC_000913	2996248 =	78 (0.830)					pseudogene (113/399 nt)	ygeO	pseudogene, orgA family, part of T3SS PAI ETT2 remnant

GCAAATCCAATAAACAATTGGAATTTACTTCCATTGATCTGTTTACTCAGTGGTTGTCACTTTTATCGAGAAAGGTTTGCAGAACGCGGGTTTTTTTATAAGGTTCCTGATGTACTAAGGGATTATTTATCAGCTATACCGCTGGAAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2996369‑2996219 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaataaTCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTAT  >  NC_000913/2996248‑2996394                                                                                                                                                                                                                                                                                                            GCAAATCCAATAAACAATTGGAATTTACTTCCATTGATCTGTTTACTCAGTGGTTGTCACTTTTATCGAGAAAGGTTTGCAGAACGCGGGTTTTTTTATAAGGTTCCTGATGTACTAAGGGATTATTTATCAGCTATACCGCTGGAAAT                                                                                                                                                       >  4:799883/1‑149    AATCCAATAAACAATTGGAATTTACTTCCATTGATCTGTTTACTCAGTGGTTGTCACTTTTATCGAGAAAGGTTTGCAGAACGCGGGTTTTTTTATAAGGTTCCTGATGTACTAAGGGATTATTTATCAGCTATACCGCTGGAAATAA                                                                                                                                                     >  2:535860/1‑148          ATAAACAATTGGAATTTACTTCCATTGATCTGTTTACTCAGTGGTTGTCACTTTTATCGAGAAAGGTTTGCAGAACGCGGGTTTTTTTATAAGGTTCCTGATGTACTAAGGGATTATTTATCAGCTATACCGCTGGAAATA                                                                                                                                                      <  1:145112/141‑1          ATAAACAATTGGAATTTACTTCCATTGATCTGTTTACTCAGTGGTTGTCACTTTTATCGAGAAAGGTTTGCAGAACGCGGGTTTTTTTATAAGGTTCCTGATGTACTAAGGGATTATTTATCAGCTATACCGCTGGAAATA                                                                                                                                                      >  2:145112/1‑141                             TTCCATTGATCTGTTTACTCAGTGGTTGTCACTTTTATCGAGAAAGGTTTGCAGAACGCGGGTTTTTTTATAAGGTTCCTGATGTACTAAGGGATTATTTATCAGCTATACCGCTGGAAA                                                                                                                                                        >  3:486644/1‑120                             TTCCATTGATCTGTTTACTCAGTGGTTGTCACTTTTATCGAGAAAGGTTTGCAGAACGCGGGTTTTTTTATAAGGTTCCTGATGTACTAAGGGATTATTTATCAGCTATACCGCTGGAAA                                                                                                                                                        <  4:486644/120‑1                                                                                                                        GGATTATTTATCAGCTATACCGCTGGAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGA                                                                         <  3:496503/108‑1                                                                                                                        GGATTATTTATCAGCTATACCGCTGGAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGA                                                                         >  4:496503/1‑108                                                                                                                              TTTATCAGCTATACCGCTGGAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGA                                                                                            <  3:178545/83‑1                                                                                                                              TTTATCAGCTATACCGCTGGAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGA                                                                                            >  4:178545/1‑83                                                                                                                                                    ATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTT    <  3:844608/149‑1                                                                                                                                                    ATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTCTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTAT                                    <  1:502848/117‑1                                                                                                                                                    ATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTCTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTAT                                    >  2:502848/1‑117                                                                                                                                                     TAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTT    >  2:220984/1‑148                                                                                                                                                       ATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTAT  >  1:109861/1‑148                                                                                                                                                       ATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTAT  <  1:585433/148‑1                                                                                                                                                                                                                                                                                                            GCAAATCCAATAAACAATTGGAATTTACTTCCATTGATCTGTTTACTCAGTGGTTGTCACTTTTATCGAGAAAGGTTTGCAGAACGCGGGTTTTTTTATAAGGTTCCTGATGTACTAAGGGATTATTTATCAGCTATACCGCTGGAAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2996369‑2996219 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaataaTCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTAT  >  NC_000913/2996248‑2996394

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ 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.