New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2068941 =	NA (NA)	23 (0.480)	22/488	1.0	56.1%	noncoding (1331/1331 nt)	IS2	repeat region
	?	NC_000913	= 2320130	18 (0.380)					coding (88/1827 nt)	atoS	sensor histidine kinase AtoS

GGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2069189‑2068941 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAAGCGTTGGGACAATGACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGCGGCGTGGATAAATCCACTTCATATAATGCATGCTGAAATCCACTAGTCTTGTCCGGTATATGACGATTATCAGAGGTTAAGGTGATGATTTCTCGGCGGTGTATCATATTCCAGAGAAGAGAGAACATTGCGGTAACACGCTTTTACCGCTACCTTAACCACACTCCATCGGTCACCTGAGGCGG  <  NC_000913/2320130‑2319889                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             GGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCATA                                                                                                                                                                                                                                                  <  1:323178/251‑1           CCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCATAAGCGTTGGGA                                                                                                                                                                                                                                        <  1:522408/251‑1           CCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAAACAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGATTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGAGGCAAATCCATAAGCGTTGGG                                                                                                                                                                                                                                         >  1:80005/1‑250                               AGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCATAAGCGTTGGGACAATGACCATCAGGATTGCC                                                                                                                                                                                                                    <  1:517487/251‑1                                    GCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAGCCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGTAAATATAGGGGCAAATCCATAAGCGTTGGGACAATGACCATCAGGATTGCCATCAG                                                                                                                                                                                                               <  2:497819/251‑1                                       TCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAGCGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCATAAGCGTTGGGACAATGACCATCAGGATTGCCATCAGG                                                                                                                                                                                                              <  2:454574/249‑1                                                        CGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCATAAGCGTTGGGACAATGACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGC                                                                                                                                                                                           >  1:227817/1‑251                                                           GACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCATAAGCGTTGGGACAATGACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGCGGC                                                                                                                                                                                        <  2:215312/251‑1                                                                    AGTATCATTCGCAAACCAGATGGGTTAACGGCAGCAAAGAAACTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCAACGGGAATATCTGCGGCAGCGGGATTGCAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCATAAGCGTTGGGACCATGACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGCGGCGTGGATAA                                                                                                                                                                                >  2:391308/1‑250                                                                                     AGACGGGTTAACGGCAGCAAAGAACCGTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCATAAGCGTTGGGACAATGACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGCGGCGTGGATAAATCCACTTCATATAATGC                                                                                                                                                              <  2:20882/251‑1                                                                                              AACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCAGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGCGATAACAGATGTCTGGAAATATAGGGGCAAATCCATAAGCGTTGGGACAATGACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGCGGCGTGGATAAATCCACTTCATATAATGCATGCTGAA                                                                                                                                                      >  1:30761/1‑250                                                                                                         AGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCATAAGCGTTGGGACAATGACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGCGGCGTGGATAAATCCACTTCATATAATGCATGCTGAAATCCACTAGTCT                                                                                                                                          >  1:4381/1‑251                                                                                                                     AGGCGTTCGAGCAGTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCATAAGCGTTGGGACAATGACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGCGGCGTGGATAAATCCACTTCATATAATGCATGCTGAAATCCACTAGTCTTGTCCGGTATAT                                                                                                                              <  2:161295/251‑1                                                                                                                        CGTTCGAGCATTATAACGAATGGTATCAGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGCAATATAGGGGCAAATCCATAAGCGTTGGGACAATGACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGCGGAGTGGATAAATCCACTTCATATAATGCATGCTGCAATCCACTAGTCTTGTCCGGTATATGAC                                                                                                                           >  2:213447/1‑251                                                                                                                         GTTCGAGCATTATAACGAATGGCATCCGCATAGGGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCATAAGCGTTGGGACAATGACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGCGGCGTGGATAAATCCACTTCATATAATGCATGCTGAAATCCACTAGTCTTGTCCGGTATATGACG                                                                                                                          <  1:64012/251‑1                                                                                                                               GCATTAGAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACTGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCATAAGCGTTGGGACAATGACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGCGGCGTGGATAAATCCACTTCATATAATGCATGCTGAAATCCACTAGTCTTGTCCGGTATATGACGATTATC                                                                                                                    <  2:386186/251‑1                                                                                                                                               CATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTCATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCATAAGCGTTGGGACAATGACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGCGGCGTGGATAAATCCACTTCATATAATGCATGCTGAAATCCACTAGTCTTGTCCGGTATATGACGATTATCAGAGGTTAAGGTGATG                                                                                                    >  1:487794/1‑251                                                                                                                                                        AGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCATAAGCGTTGGGACAATGACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGCGGCGTGGATAAATCCACTTCATATAATGCATGCTGAAATCCACTAGTCTTGTCCGGTATATGACGATTATCAGAGTTTAAGGTGATGATTTCTCG                                                                                            <  1:172983/250‑1                                                                                                                                                                 GGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCATAAGCGTTGGGACAATGACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGCGGCGTGGATAAATCCACTTCATATAATGCATGCTGAAATCCACTAGTCTTGTCCGGTATATGACGATTATCAGAGGTTAAGGTGATGATTTCTCGGCGGTGTATC                                                                                  <  2:523401/251‑1                                                                                                                                                                 GGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCATAAGCGTTGGGACAATGACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGCGGCGTGGATAAATCCACTTCATATAATGCATGCTGAAATCCACTAGTCTTGTCCGGTATATGACGATTATCAGAGGTTAAGGTGATGATTTCTCGGCGGTGTATC                                                                                  <  2:441608/251‑1                                                                                                                                                                                                               GGTTAAGTGATAACAGATGTCTGGAAAGATAGGGGCAAATCCATAAGCGTTGGGACAATGACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGCGGCGTGGATAAATCCACTTCATATAATGCATGCTGAAATCCACTAGTCTTGTCCGGTATATGACGATTATCAGAGGTTAAGGTGATGATTTCTCGGCGGTGTATCATATTCCAGAGAAGAGAGAACATTGCGGTAACACGCTTTTACCGCT                                    <  1:375868/251‑1                                                                                                                                                                                                                                     tGAAATATAGGGGCAAATCCATAAGCGTTGGGACAATTACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGCGGCGTGGATAAATCCACTTCATATAATGCATGCTGAAATCCACTAGTCTTGTCCGGTATATGACGATTATCAGAGGTTAAGGTGATGATTTCTCGGCGGTGTATCATATTCCAGAGAAGATAGAACATTGCGGTAACACGCTTTTACCGCTACCTTAACCACACTCCATC                 <  1:213447/247‑1                                                                                                                                                                                                                                                 GCAAATCCATAAGCGTTGGGACAATGACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGCGGCGTGGATAAATCCACTTCATATAATGCATGCTGAAATCCACTAGTCTTGTCCGGTATATGACGATTATCAGAGGTTAAGGTGATGATTTCTCGGCGGTGTATCATATTCCAGAGAAGAGCGAACATTGCGGTAACACGCTTTTACCGCTACCTTAACAACACTCCATCGGTCACCTGAGGCGG  >  1:209032/1‑251                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             GGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2069189‑2068941 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAAGCGTTGGGACAATGACCATCAGGATTGCCATCAGGATCATTTGATTGCGTAAGCGGCGTGGATAAATCCACTTCATATAATGCATGCTGAAATCCACTAGTCTTGTCCGGTATATGACGATTATCAGAGGTTAAGGTGATGATTTCTCGGCGGTGTATCATATTCCAGAGAAGAGAGAACATTGCGGTAACACGCTTTTACCGCTACCTTAACCACACTCCATCGGTCACCTGAGGCGG  <  NC_000913/2320130‑2319889

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ 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.