New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_pgi	= 1636407	20 (0.900)	4 (0.200)	4/252	2.3	17.9%	intergenic (‑40/‑349)	nohQ/ynfO	pseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin/uncharacterized protein, Qin prophage
	?	NC_000913_3_vch_pgi	= 1636432	19 (0.960)					intergenic (‑65/‑324)	nohQ/ynfO	pseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin/uncharacterized protein, Qin prophage
Rejected: Frequency below/above cutoff threshold.

ATTCCCTGTTCCTGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACCTGTCGTTTCCTTTCTTTTCAGGGGGTATTTTAAATAAAAACATTAAGTTACGACGAAGAAGAACGGAAATGCCTTAAACCGGAAAATTTTCATAAATAGCGAAAACCCGCGAGGTCGCCGCCCCGTAACCTGTCG  >  NC_000913_3_vch_pgi/1636288‑1636568                                                                                                                                                 |                                                                                                                                         agtccCTGTTCCTGCCAGTTCTGAATGGTACGGATAATGGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCGAAAAACAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACctgt                                                                                                                                      >  2:116603‑M2/3‑145 (MQ=255)      cTGTTCCTGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACctgtcgttt                                                                                                                                 <  1:319605‑M2/149‑10 (MQ=255)            cTGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACctgtcgtttcctttc                                                                                                                           <  1:126286‑M2/149‑16 (MQ=255)                   tgcggAATGGTACGGATACCCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACCTGTCGTTTCCTTTCTTTTCAg                                                                                                                    <  1:313974/145‑1 (MQ=255)                                ggctACTTGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACCTGTCGTTTCCTTTCTTTTCAGTGGGTATTTtaaa                                                                                                       <  2:46624/146‑1 (MQ=255)                                ggATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACCTGTCGTTTCCTTTCTTTTCAGGGGGTATTTtaaa                                                                                                       <  2:37290/149‑1 (MQ=255)                                ggATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACCTGTCGTTTCCTTTCTTTTCAGGGGGTATTTtaaa                                                                                                       >  2:259468/1‑149 (MQ=255)                                                                 ttttGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACCTGTCGTTTCCTTTCTTTTCAGGGGGTATTTTAAATAAAAACATTATATTACGCCATAGAAGAACGGa                                                                      >  2:92174/1‑149 (MQ=14)                                                                 ttttGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACCTGTCGTTTCCTTTCTTTTCAGGGGGTATTTTAAATAAAAACATTAAGTTACGACGAAGAAAAACGGa                                                                      >  1:168969/1‑149 (MQ=255)                                                                 gtttGTCGAATGCCATTGTTAATTTCACGGGCAAAAACAGAGAAAGGAAATCACAGAGGCCCAAAAGCTCGTTTTCATCACCTGTCGTTTTCTTTCTTTTCAGGGGGTATTTTAAATAAAAACATTAAGTTACGACGAAGAAGAACGGa                                                                      <  2:174718/148‑1 (MQ=14)                                                                      ttgACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACCTGTCGTTTCCTTTCTTTTCAGGGGGTATTTTAAATAAAAACATTAAGTTACGAGGAAGAAAAACGGAAATGc                                                                 >  1:231493/1‑149 (MQ=255)                                                                       cgACATCCATTGGTCATTCCACCGCCAAAAACAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACCTGTCGTTTCCTTTCTTTTCACGGGGTATTTTAAATAAAAACATTAAGTTACGACGAAGAAGAACGGAAATGcc                                                                <  1:92174/148‑1 (MQ=255)                                                                        gACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACCTGTCGTTTCCTTTCTTTTCAGGGGGTATTTTAAATAAAAACATTAAGTTACGACGAAGAAGAACGGAAATGCCt                                                               <  1:259468/149‑1 (MQ=255)                                                                             ccATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACCTGTCGTTTCCTTTCTTTTCAGGGGGTATTTTAAATAAAAACATTAAGTTTAGACAAAGAAGAACGCAAATGcgtgaacc                                                          >  1:236648/1‑142 (MQ=17)                                                                                ttGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACCTGTCGTTTCCTTTCTTTTCAGGGGGTATTTTAAATAAAAACATTAAGTTACGACGAAGAAGAACGGAAATGCCTTAAACCgg                                                       >  1:23113/1‑149 (MQ=255)                                                                                   ttCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACCAGTCGTTTCCTTTCTTTTCAGGGGGTATTTTAAATAAAAACATTAAGTTACGACGAAGAAGAACGGAAATGCCTTAAACCGGaaa                                                    >  2:93441/1‑149 (MQ=255)                                                                                    tCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACCTGTCGTTTCCTTTCTTTTCAGGGGGTATTTTAAATAAAAACATTAAGTTACGACGAAGAAGAAGGGAAATGCCTTAAACCGGaaaa                                                   >  1:33335/1‑149 (MQ=255)                                                                                                 aaaaaCAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACCTGTCGTTTCCTTTCTTTTCAGGGGGTATTTTAAATAAAAACATTAAGTTACGACGAAGAAGAACGGAAATGCCTTAAACCGGAAAATTTTCATAAATAg                                      >  1:72078/1‑149 (MQ=255)                                                                                                     aCAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACctatcgtttcctttctctgt                                                                                                                      <  1:351722‑M2/65‑21 (MQ=255)                                                                                                     aCAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACctatcgtttcctttctctgt                                                                                                                      >  2:351722‑M2/1‑45 (MQ=255)                                                                                                                 aaCGACAGAGGCCCAAAAGCTCGTTTTCAGCACctgtcgtttcctttctctgtttttggccgtggaatgaacaatggaagtcaacaaaaagcagctggctgacattttcggtgcgagtatccgtaccattcagaactggcaggaacag                       <  1:314434‑M2/148‑116 (MQ=255)                                                                                                                 aaCGACAGAGGCCCAAAAGCTCGTTTTCAGCACctgtcgtttcctttctctgtttttggccgtggaatgaacaatggaagtcaacaaaaagcagctggctgacattttcggtgcgagtatccgtaccattcagaactggcaggaacag                       >  2:314434‑M2/1‑33 (MQ=255)                                                                                                                 aaCGACAGAGGCCCAAAAGCTCGTTTTCAGCAACTGTCGTTTCCTTGCGTTTAAGGGGGGATTTTAAATATAAAGATTAAGTTACGAGCAAGAAAACGGGAAATACATAAACCCGGAAAATTTGCCTAAATAGCGAAAAAACGCGAGGt                      >  2:187453/1‑149 (MQ=255)                                                                                                                  aCGACAGAGGCCCAAAAGCTCGTTTTCAGCACCTGTCGTTTCCTTTCTTTTCAGGGGGTATTTTAAATAAAAACATTAAGTGACGACGAAGAAGAACGGCAATGCCTGAAACGGGAAAATGTTCATAAGTAGCGAAAACCCGCGAGGTc                     >  1:10760/1‑149 (MQ=14)                                                                                                                                    cTCGTTTTCAGCACCTGTCGTTTCCTTTCTTTTCAGGGGGTATTTTAAATAAAAACATTAAGTTACGACGAAGAAGAACGGAAATGCCTTAAACCGGAAAATTTTCATAAATAGCGAAAACCAGCGAGGCGGACGCCCCGTAAACCGTc   >  2:92201/1‑149 (MQ=14)                                                                                                                                     tCGTTTTCAGCACCTGTCGTTTCCTTTCTTTTCAGGGGGTATTTTAAATAAAAACATTAAGTTACGACGAAGAAGAACGGAAATGCCTTAAACCGGAAAATTTTCATAAATAGCGAAAACCCGCGAGGTCGCCGCCCCGTAACCTGTCg  >  2:12172/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                         ATTCCCTGTTCCTGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGAGGCCCAAAAGCTCGTTTTCAGCACCTGTCGTTTCCTTTCTTTTCAGGGGGTATTTTAAATAAAAACATTAAGTTACGACGAAGAAGAACGGAAATGCCTTAAACCGGAAAATTTTCATAAATAGCGAAAACCCGCGAGGTCGCCGCCCCGTAACCTGTCG  >  NC_000913_3_vch_pgi/1636288‑1636568

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.