New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	1207790 =	33 (0.910)	5 (0.150)	5/248	3.8	13.8%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913_3_pae_tpiA	1209619 =	33 (1.020)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GCAGCGTGGTGGAGGCATCCGGTGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGG  >  NC_000913_3_pae_tpiA/1207643‑1207938                                                                                                                                                    |                                                                                                                                                     gCAGCGTGGTGGAGGCATCCGGTGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCAAAAACCtt                                                                                                                                                     >  1:562221/1‑149 (MQ=255)    gCGTGGTGGAGGCATCCGGTGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGt                                                                                                                                                  >  1:324445/1‑149 (MQ=255)        ggtggAGGCATCCGGTGCCAGCCTGGAGAAGGGGCGGCATGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCCGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTgg                                                                                                                                              <  2:327203/149‑1 (MQ=255)              ggctgtcGGTGCCAGCCCGGGGAAGGGGCGGAAAGAGCAGTTACGTACCGCACTTCCCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAg                                                                                                                                        <  2:93174/143‑1 (MQ=17)               gCATCCGGTGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAgg                                                                                                                                       >  1:256859/1‑149 (MQ=255)                cATCGGGGGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGa                                                                                                                                      <  2:249277/149‑1 (MQ=255)                cATCCGGTGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGa                                                                                                                                      <  1:636642/149‑1 (MQ=255)                 aTCCGGTGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAg                                                                                                                                     >  2:403211/1‑149 (MQ=255)                         ccAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTc                                                                                                                             <  2:380428/149‑1 (MQ=255)                              cTGGACATGGGGCGCCACGATCAGTTACTTACCCCACTACGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAACCGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATgc                                                                                                                        <  1:133889/149‑1 (MQ=18)                               tgtagaATGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATgca                                                                                                                       <  1:276901/146‑1 (MQ=255)                                gcattaGGGGCAACACGCCCACCTACTTACCGCACTGCGCGCGCTGGTGGCAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATgcag                                                                                                                      <  2:602306/144‑1 (MQ=18)                                            gcACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACAt                                                                                                          <  1:348170/149‑1 (MQ=255)                                                   cAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACg                                                                                                   <  1:28687/149‑1 (MQ=255)                                                      ttacttacCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCAc                                                                                                >  1:343191/1‑149 (MQ=255)                                                                cACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATa                                                                                      <  1:403211/149‑1 (MQ=255)                                                                 accttgcgcgcTGCTGTTAAGCCGCAAAAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCCATTGATAGTCCAAAACCTTAAGTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAg                                                                                     <  1:152710/144‑1 (MQ=25)                                                                 aCTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAg                                                                                     <  1:120949/149‑1 (MQ=255)                                                                   ttCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACAGCTCTCGAAAACCTTGGTAGCGGATCGATAACGTTAGTGTAGGCAACAACGTCTACATTAGGACGCACCGGTTTGATAGcc                                                                                   >  2:457619/1‑148 (MQ=9)                                                                           ctgctgTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTAGAAAACCTTGGTTTGGGAGAAGGAGCAAACCTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTGATAGCTATACCGGt                                                                           >  2:628911/1‑149 (MQ=255)                                                                                 ttAAGCCGCAAGAAGCCGTTTGGCCATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGAt                                                                     >  1:553047/1‑149 (MQ=255)                                                                                  tAAGCCGCAAGAATCCGATTGGCAATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGAtt                                                                    <  1:511417/149‑1 (MQ=255)                                                                                    aGCCGCAAGAATCCGTTTGGCGATACCAAATCGGATGGCACTGAGCAAACGGCTCTCGAAAACCTTGGTATGGGAGAAGGAGCAAAACTCAATGCAGCAACTGCTACATAAGGACGCACCGGTTTCATAGCTATACCGGTTATGATtgg                                                                  >  1:489070/1‑149 (MQ=38)                                                                                             aaTCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGa                                                         <  1:270235/149‑1 (MQ=255)                                                                                                             tCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACgg                                                                                                                <  2:166896/78‑1 (MQ=255)                                                                                                             tCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACgg                                                                                                                >  1:166896/1‑78 (MQ=255)                                                                                                                     gATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTgggg                                 >  2:167702/1‑149 (MQ=255)                                                                                                                               tgCAATAGGGTCTCGAAAAGCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGcc                       <  2:21158/149‑1 (MQ=255)                                                                                                                               tgCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGcc                       >  1:47436/1‑149 (MQ=255)                                                                                                                                   aaCGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCaa                   >  1:201671/1‑149 (MQ=255)                                                                                                                                      ggCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAg                >  1:375966/1‑149 (MQ=255)                                                                                                                                           tcGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAg                                                                                     >  2:383737/1‑75 (MQ=255)                                                                                                                                           tcGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAg                                                                                     <  1:383737/75‑1 (MQ=255)                                                                                                                                                    ttGGTTTGGGAGAAGGAGCAAAAATCAATGCAGCAGAGGCTACATTATGACTCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTggg  <  2:299161/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                     GCAGCGTGGTGGAGGCATCCGGTGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGG  >  NC_000913_3_pae_tpiA/1207643‑1207938

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ 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.