New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 3535513	138 (1.210)	3 (0.030)	3/412	NT	2.3%	coding (354/1353 nt)	envZ	sensory histidine kinase in two‑component regulatory system with OmpR
	?	NC_000913	= 3535631	123 (1.130)					coding (236/1353 nt)	envZ	sensory histidine kinase in two‑component regulatory system with OmpR
Rejected: Frequency below/above cutoff threshold.

CCCTTTACCAACCTGCAAGGCTGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGCGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3535270‑3535513 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttccgtcgggAGATCTACCGTGAGCTGGGGATCTCTCTCTACTCCAACGAGGCTGCCGAAGAGGCAGGTCTGCGTTGGGCGCAACACTATGAATTCTTAAGCCATCAGATGGCGCAGCAACTGGGCGGCCCGACGGAAGTGCGCGTTGAGGTCAACAAAAGTTCGCCTGTCGTCTGGCTGAAAACCTGGCTGTCGCCCAATATCTGGGTACGCGTGCCGCTGACCGAAATTCATCAGGGCGA  <  NC_000913/3535631‑3535400                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              CCCTTTACCAACCTGCAAGGCTGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGCGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCG                                                                                                                                                                                                                                               <  1:1158451/239‑1  CCTTTACCAACCTGCAAGGCTGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGCGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCG                                                                                                                                                                                                                                               >  2:790818/1‑238                                    CGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGCGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGAGATCTACCGTGAGCTGGGGATCTCTCTCT                                                                                                                                                                                                            >  2:989107/1‑239                                                                                                                    AACAGCGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGAGATCTACCGTGAGCTGGGGATCTCTCTCTACTCCAACGAGGCTGCCGAAGAGGCAGGTCTGCGTTGGGCGCAACACTATGAATTCTTAAGCCATCAGATGGCGCAGCA                                                                                                                             <  1:989107/238‑1                                                                                                                                                                                GGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGAGATCTACCGTGAGCTGGGGATCTCTCTCTACTCCAACGAGGCTGCCGAAGAGGCAGGTCTGCGTTGGGCGCAACACTATGAATTCTTAAGCCATCAGATGGCGCAGCAACTGGGCGGCCCGACGGAAGTGCGCGTTGAGGTCACCAAAAGTTCGCCTGTCGTCTGGCTG                                                                >  1:474040/1‑239                                                                                                                                                                                                                                           gTCCGTCGGGAGATCTACCGTGAGCTGGGGATCTCTCTCTACTCCAACGAGGCTGCCGAAGAGGCAGGTCTGCGTTGGGCGCAACACTATGAATTCTTAAGCCATCAGATGGCGCAGCAACTGGGCGGCCCGACGGAAGTGCGCGTTGAGGTCAACAAAAGTTCGCCTGTCGTCTGGCTGAAAACCTGGCTGTCGCCCAATATCTGGGTACGCGTGCCGCTGACCGAAATTCATCAGGG     <  2:646216/238‑1                                                                                                                                                                                                                                           TTCCGTCGGGAGATCTACCGTGAGCTGGGGATCTCTCTCTACTCCAACGAGGCTGCCGAAGAGGCAGGTCTGCGTTGGGCGCAACACTATGAATTCTTAAGCCATCAGATGGCGCAGCAACTGGGCGGCCCGACGGAAGTGCGCGTTGAGGTCAACAAAAGTTCGCCTGTCGTCTGGCTGAAAACCTGGCTGTCGCCCAATATCTGGGTACGCGTGCCGCTGACCGAAATTCATCAGG      >  2:259299/1‑238                                                                                                                                                                                                                                            TCCGTCGGGAGATCTACCGTGAGCTGGGGATCTCTCTCTACTCCAACGAGGCTGCCGAAGAGGCAGGTCTGCGTTGGGCGCAACACTATGAATTCTTAAGCCATCAGATGGCGCAGCAACTGGGCGGCCCGACGGAAGTGCGCGTTGAGGTCAACAAAAGTTCGCCTGTCGTCTGGCTGAAAACCTGGCTGTCGCCCAATATCTGGGTACGCGTGCCGCTGACCGAAATTCATCAGGGC    <  1:523998/239‑1                                                                                                                                                                                                                                              CGTCGGGAGATCTACCGTGAGCTGGGGATCTCTCTCTACTCCAACGAGGCTGCCGAAGAGGCAGGTCTGCGTTGGGCGCAACACTATGAATTCTTAAGCCATCAGATGGCGCAGCAACTGGGCGGCCCGACGGAAGTGCGCGTTGAGGTCAACAAAAGTTCGCCTGTCGTCTGGCTGAAAACCTGGCTGTCGCCCAATATCTGGGTACGCGTGCCGCTGACCGAAATTCATCAGGGCGA  <  1:1052933/239‑1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              CCCTTTACCAACCTGCAAGGCTGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGCGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3535270‑3535513 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttccgtcgggAGATCTACCGTGAGCTGGGGATCTCTCTCTACTCCAACGAGGCTGCCGAAGAGGCAGGTCTGCGTTGGGCGCAACACTATGAATTCTTAAGCCATCAGATGGCGCAGCAACTGGGCGGCCCGACGGAAGTGCGCGTTGAGGTCAACAAAAGTTCGCCTGTCGTCTGGCTGAAAACCTGGCTGTCGCCCAATATCTGGGTACGCGTGCCGCTGACCGAAATTCATCAGGGCGA  <  NC_000913/3535631‑3535400

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 30 ≤ 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.