New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_pgi	= 4466372	17 (0.880)	3 (0.160)	3/274	2.5	17.1%	coding (878/948 nt)	treR	trehalose 6‑phosphate‑inducible trehalose regulon transcriptional repressor
	?	NC_000913_3_vch_pgi	= 4466464	13 (0.710)					coding (786/948 nt)	treR	trehalose 6‑phosphate‑inducible trehalose regulon transcriptional repressor
Rejected: Frequency below/above cutoff threshold.

GGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCG‑TTGCTCTTGCAGGTATTTACTTGCGCCAAGTGCCAGCGTGTCGGTTGCGCACAGTAAGGCGGTAGTTTCAGGCGTAATCACTTTTGCAACGTTCTCATAGCCTTGCTTCATAG  >  NC_000913_3_vch_pgi/4466318‑4466600                                                                                                                                                   |                                                                                                                                          gggATGATGCTTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCCAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTCCGGTTACGATCTCCGGCTGGAGGCATTTCATTAACGGCGTTTTTCCTccgcccgc                                                                                                                                         >  2:163442/1‑149 (MQ=255) gggATGATGATTTGTTGAGGTTCGCTGCGCACGGTTACCTGCGAGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTAATTAGCGGCGTGTTCGCGACGCTCgc                                                                                                                                         <  1:92580‑M2/149‑3 (MQ=255)      gatgatTTGTTGCGGTTGGCTACGCCCGGTTACCTGCGCGATCCACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAAACGGGATCTACGGCTCCGATCTCGGGATGGAGGAATTTCAGTACCGGCGCATTTCCGACGCCCgcccgtt                                                                                                                                    <  2:18533‑M2/149‑8 (MQ=255)      gatgatTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCgccagtt                                                                                                                                    <  1:140450‑M2/149‑8 (MQ=255)        tgatTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGCCGCTCGCCAGTTGc                                                                                                                                  >  1:237623/1‑149 (MQ=255)               ttgCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGAATTACCGACGCTCgccagttgaaaggggt                                                                                                                           <  1:176834‑M2/149‑17 (MQ=255)                tgCGGTTCGCGGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTc                                                                                                                          <  1:63946/149‑1 (MQ=255)                                        tGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCG‑TTGCTCTTGCGGGTCttt                                                                                                 >  2:217358/1‑149 (MQ=255)                                            cgATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCACGGTGTCGATGCG‑TTGATCTTGCAGGTATTTACtt                                                                                             >  1:71969/1‑149 (MQ=255)                                             gATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCgccagttgatcgcgcaggtaaccgggcgcagcgaaccgcaacaaat                                                                                             <  2:261320‑M2/149‑47 (MQ=255)                                               tCAACTCGCAAGCCGCCTGGCGTCCAGCTGACTCGTAACCGGGATCTCCGTTTACGATCACCGGATGGAGGAACGTCAGGATCGGCGTATTGCCGAAGCTAGCCGGTTCGAAGGTGGCCA‑GCGCGTGCTCTTGCCGGTCGTTACtgcct                                                                                          >  2:39258/1‑145 (MQ=255)                                                                 gccctCCGGCGTCGGCGTAACCGCGATCTACGGTTACTATCGCCGGATGGAGGAATTTCATGAAGGGCGTATTTGAGGCGCTCGCCGGGTGCACGGTGCCGATGCC‑GTGCTCTTGCAGGTATTTACTTGCGCCAAGCGCCAGCGTGTCg                                                                        <  2:209102/145‑1 (MQ=255)                                                                    ggccAGCTTGGGGGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCG‑TTGCTCTTGCAGGTATTTACTTGCGCCAAGTGCCAGCGTGTCGGtt                                                                     <  2:247192/147‑1 (MQ=255)                                                                                cGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCG‑TTGCTCTTGCAGGTATTTACTTGCGCCAAGTGCCAGCGTGTCGGTTGCGCACAGTAAg                                                         <  1:184064/149‑1 (MQ=255)                                                                                  tAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCG‑TTGCTCTTGCAGGTATTTACTTGCGCCAAGTGCCCGCGTGTCGGTTGCGCACAGTAAGGc                                                       >  2:198353/1‑149 (MQ=255)                                                                                                   tACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCgccagttgatcgcgcaggtaaccgggcgcagcgaaccgcaacaaatcatcatccccgccaccctgtcctgatcgtttcctgaacgataaattgtgatctt                                       >  1:261320‑M2/1‑49 (MQ=255)                                                                                                          tcCGGATGGACGAAATTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCG‑TTGCTCTTGCAGGTATTTACTTGCGCCAAGGCCCAGCGTGTCGGTTGCGCACCGTAGGGCGGTAGTTTCAGCCGTAATCACttg                               >  2:176768/1‑148 (MQ=255)                                                                                                                           cATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCG‑TTGCTCTTGCAGGTATTTACTTGCGCCAAGTGCCAGCGTGTCGGTTGCGCACAGTAAGGCGGCGCGTTCCGGCGTAATCACTTTTGTCACGTTCTCATAGc              >  2:147475/1‑149 (MQ=255)                                                                                                                                      gaTTACGGGCGATCGCAAGTTGGAAGGTGTCGATGCG‑TTGCTCCTGCAGGTATTTACGTGCTACAAGCGCCAGCGTTTCGGCTGCTCACAAGAAGGCGGTAGTCTCAGGCGTAATCACTTTTGCAACGATCTCATAGCCTTGCTTCATa   <  2:237230/148‑1 (MQ=255)                                                                                                                                       atcccggACGCTCGCCAGGTGCAAGGTGTCGATGCG‑TTGGTCTTGCAGGTATTTACTTGCGCCAAGTGCCAGCGTGTCGGTTGCGCACAGTAAGGCGGTAGTTTCAGGCGTAATCACTTTTGCAACGTTCTCACAGCCTTGACTCATAg  <  2:26747/143‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                          GGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCG‑TTGCTCTTGCAGGTATTTACTTGCGCCAAGTGCCAGCGTGTCGGTTGCGCACAGTAAGGCGGTAGTTTCAGGCGTAATCACTTTTGCAACGTTCTCATAGCCTTGCTTCATAG  >  NC_000913_3_vch_pgi/4466318‑4466600

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.