New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 3167879	21 (1.210)	3 (0.190)	3/254	2.1	13.5%	coding (368/396 nt)	mqsA	antitoxin for MqsR toxin; transcriptional repressor
	?	NC_000913_3_pae_pgi	= 3167883	19 (1.170)					coding (364/396 nt)	mqsA	antitoxin for MqsR toxin; transcriptional repressor
Rejected: Frequency below/above cutoff threshold.

GGAGAAATTATAAGCCCAACAACAATACGCCTGTGGCATTGTTCGCTCAAACTTATCGCGAGTGATTTGGCTCACACTCCGGTAAAGAAAAAAGCGAGTTGCCCCCGCTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATGCTTATCCAGAACACGTAAAAGTTTGATTGTGGAAGGATGAGGTTGGGCATTGCCTTTTTCGTAACGCGAAAACGCATTTACACCTCCCCCAAAAATTTCGCTTGCCTCTTTTTGGGTAAGAGAGAGCTTTTTTCGAACCTTCACTA  >  NC_000913_3_pae_pgi/3167732‑3168026                                                                                                                                                    |                                                                                                                                                    ggAGAAATTATAAGCCCAACAACAATACGCCTGTGGCATTGTTCGCTCAAACTTATCGCGAGTGATTTGGCTCACACTCCGGTAAAGAAAAAAGCGAGTTGCCCCCGCTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATGc                                                                                                                                                   >  2:3088/1‑150 (MQ=255)      aaTTATAAGCCCAACAACAATACGCCTGTGTCATTGTTCGCTCAAACTTATCGCGAGTGATTTGGCTCACACTCCGGTAAAGAAAAAAGCGAGTTGCCCCCGCTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATGCTTatc                                                                                                                                              >  2:35078‑M2/1‑147 (MQ=255)                     aacaaTACGCCTGTGGCATTGTTCGCTCAAACTTATCGCGAGTGATTTGGCTCACACTCCGGTAAAGAAAAAAGCGAGTTGCCCCCGCTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATGCTTATACAGAACACGTAAAAg                                                                                                                               >  2:78515/1‑150 (MQ=255)                           aCGCCTGTGGCATTGTTCGCTCAAACTTATCGCGAGTGATTTGGCTCACACTCCGGTAAAGAAAAAAGCGAGTTGCCCCCGCTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATGc                                                                                                                                                   >  1:21174/1‑124 (MQ=255)                           aCGCCTGTGGCATTGTTCGCTCAAACTTATCGCGAGTGATTTGGCTCACACTCCGGTAAAGAAAAAAGCGAGTTGCCCCCGCTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATGc                                                                                                                                                   <  2:21174/124‑1 (MQ=255)                              ccTGTGGCATTGTTCGCTCAAACTTATCGCGAGTGATTTGGCTCACGCTCCGGTAAAGAAAAAAGCGAGTTGCCCCCGCTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATaagcatccagaactattgaatgaaatccgtt                                                                                                                      <  3:94315‑M1/150‑32 (MQ=255)                               cTGTGGCATTGTTCGCTCAAACTTATCGCGAGTGATTTGGCTCACACTCCGGTAAAGAAAAAAGCGAGTTGCCCCCGCTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATGCTTATCCAGAACACGTAAAAGTTTGATtgtg                                                                                                                     <  2:167186/150‑1 (MQ=255)                                      aTTGTTCGCTCAAACTTATCGCGAGTGATTTGGCTCACACTCCGGTAAAGAAAAAAGCGAGTTGCCCCCGCTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATGCTTATCCAGAACACGTAAAAGTTTGATTGTGGAAGGAt                                                                                                              >  3:119095/1‑150 (MQ=255)                                              cTCAAACTTATCGCGAGTGATTTGGCTCACACTCCGGTAAAGAAAAAAGCGAGTTGCCCCCGCTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATGCTTATCCAGAACACGTAAAAGTTTGATTGTGGAAGGATGAGGTTgg                                                                                                      <  4:119095/150‑1 (MQ=255)                                                   aCTTATCGCGAGTGATTTGGCTCACACTCCGGTAAAGAAAAAAGCGAGTTGCCCCCGCTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATGCTTATCCAGAACACGTAAAAGTTTGATTGTGGAAGGATGAGGTTGGGCAtt                                                                                                 <  1:61984/150‑1 (MQ=255)                                                             aGTGATTTGGCTCACACTCCGGTAAAGAAAAAAGCGAGTTGCCCCCGCTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATGCTTATCCAGAACACGTAAAAGTTTGATTGTGGAAGGATGAGGTTGGGCATTGCCTTTTTCg                                                                                       >  1:196580/1‑150 (MQ=255)                                                                                 ggTAAAGAAAAAAGCGAGTTGCCCCCGGTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATGCTTATCCAGAACACGTAAAAGTTTGATTGTGGAAGGATGAGGTTGGGCATTGCCTTTTTCGTAACGCGAAAACGCATTTac                                                                   >  1:142036/1‑150 (MQ=255)                                                                                                 aGTTGCCCCCGCTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATaagcatccagaactattgaatgaaatccgttaa                                                                                                                    <  4:58920‑M1/85‑34 (MQ=255)                                                                                                 aGTTGCCCCCGCTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATaagcatccagaactattgaatgaaatccgttaa                                                                                                                    >  3:58920‑M1/1‑52 (MQ=255)                                                                                                 aGTTGCCCCCGCTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATGCTTATCCAGAACACGTAAAAGTTTGATTGTGGAAGGATGAGGTTGGGCATTGCCTTTTTCGTAACGCGAAAACGCATTTACACCTCCCCCAAAAAtt                                                   >  2:1818/1‑150 (MQ=255)                                                                                                      cccccGCTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATGCTTATCCAGAACACGTaaaa                                                                                                                                >  1:156787/1‑68 (MQ=255)                                                                                                      cccccGCTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATGCTTATCCAGAACACGTaaaa                                                                                                                                <  2:156787/68‑1 (MQ=255)                                                                                                                  cATTAATTAACGGATTTCATTCAATAGTTCTGGATGCTTATCCAGAACACATAAAAGTTTGATTGTGGAAGGATGAGGTTGGGCATTGCCTTTTTCGTAACGCGAAAACGCATTTACACCTCCCCCAAAAATTTCGCTTGCCTCTTTTTg                                  <  1:3088/150‑1 (MQ=255)                                                                                                                   attaattaACGGATTTCATTCAATAGTTCTGGATGCTTATCCAGAACACGTAAAAGTTTGATTGTGGAAGGCTGAGGTTGGGCATTGCCTTTTTCGTAACGCGAAAACGCATTTACACCTCCCCCAAAAATTTCGCTTGCCTCTTTTTgg                                 <  2:146742/150‑1 (MQ=255)                                                                                                                        ttaaCGGATTTCATTCAATAGTTCTGGATGCTTatccagaactattgaatgaaatccgttaattaatggaaaagcgggggcaact                                                                                             >  3:58920‑M2/1‑33 (MQ=255)                                                                                                                        ttaaCGGATTTCATTCAATAGTTCTGGATGCTTatccagaactattgaatgaaatccgttaattaatggaaaagcgggggcaact                                                                                             <  4:58920‑M2/85‑53 (MQ=255)                                                                                                                          aaCGGATTTCATTCAATAGTTCTGGATGCTTatccagaactattgaatgaaatccgttaattaatggaaaagcgggggcaactcgcttttttctttaccggagcgtgagccaaatcactcgcgataagtttgagcgaacaatgccacagg                          <  3:94315‑M2/150‑120 (MQ=255)                                                                                                                              gATTTCATTCAATAGTTCTGGATGCTTATCCAGAACACGTAAAAGTTTGATTGTGGAAGGATGAGGTTGGGCATTGCCTTTTTCGTAACGCGAAAACGCATTTACACCTCCCCCAAAAATTTCGCTTGCCTCTTTTTGGGTAagagagag                      <  1:78515/150‑1 (MQ=255)                                                                                                                                    attcaATAGTTCTGGATGCTTATCCAGAACACGTAAAAGTTTGATTGTGGAAGGATGAGGTTggg                                                                                                     <  2:189546/65‑1 (MQ=255)                                                                                                                                    attcaATAGTTCTGGATGCTTATCCAGAACACGTAAAAGTTTGATTGTGGAAGGATGAGGTTggg                                                                                                     >  1:189546/1‑65 (MQ=255)                                                                                                                                      tcaATAGTTCTGGATGCTTATCCAGAACACGTAAAAGTTTGATTGTGGAAGGATGAGGTTGGGCATTGCCTTTTTCGTAACGCGAAAACGCATTTACACCTCCCCCAAAAATTTCGCTTGCCTCTTTTTGGGTAAGAGAGAGCTTTTTTc              <  3:5290/150‑1 (MQ=255)                                                                                                                                             ttCTGGATGCTTATCCAGAACACGTAAAAGTTTGATTGTGGAAGGATGAGGTTGGGCATTGCCTTTTTCGTAACGCGAAAACGCATTTACACCTCCCCCAAAAATTTCGCTTGCCTCTTTTTGGGTAAGAGAGAGCTTTTTTCGAACCtt       >  2:116691/1‑150 (MQ=255)                                                                                                                                                 ggATGCTTATCCAGAACACGTAAAAGTTTGATTGTGGAAGGATGAGGTTGGGCATTGCCTTTTTCGTAACGCGAAAACGCATTTACACCTCCCCCAAAAATTTCGCTTGCCTCTTTTTGGGTAAGAGAGAGCTTTTTTCGAACCTTCACt   >  3:60133/1‑150 (MQ=255)                                                                                                                                                  gATaagcatccagaactattgaatgaaatccgttaattaatggaaaagcgggggcaactcgcttttttctttaccggagtgtgagccaaatcactcgcgataagtttgagcgaacaatgacacaggcgtattgttgttgggcttataatt  >  2:35078‑M1/1‑3 (MQ=255)                                                                                                                                                    |                                                                                                                                                    GGAGAAATTATAAGCCCAACAACAATACGCCTGTGGCATTGTTCGCTCAAACTTATCGCGAGTGATTTGGCTCACACTCCGGTAAAGAAAAAAGCGAGTTGCCCCCGCTTTTCCATTAATTAACGGATTTCATTCAATAGTTCTGGATGCTTATCCAGAACACGTAAAAGTTTGATTGTGGAAGGATGAGGTTGGGCATTGCCTTTTTCGTAACGCGAAAACGCATTTACACCTCCCCCAAAAATTTCGCTTGCCTCTTTTTGGGTAAGAGAGAGCTTTTTTCGAACCTTCACTA  >  NC_000913_3_pae_pgi/3167732‑3168026

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ 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.