New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	644022 =	33 (1.030)	6 (0.200)	5/268	3.6	17.6%	intergenic (‑55/+175)	rnk/rna	regulator of nucleoside diphosphate kinase/ribonuclease I
	?	NC_000913_3_pae_tpiA	644051 =	25 (0.830)					intergenic (‑84/+146)	rnk/rna	regulator of nucleoside diphosphate kinase/ribonuclease I
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CGATTGGCAAACCAGCATAGGCGGGTTGCTCCAGCAGAATATCGATGCGTTCGGCATCCAGGTCGTTAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGTTTAACTCACATGATGATACTGACTGTTGCTCACTCTTTGAAGTGATTTGCGTCACATTCAGGGAATTCCTCAATGCAGCGCATTATGTATAAATCTTAATCGCCTTGGTTTATGGAA  >  NC_000913_3_pae_tpiA/643877‑644165                                                                                                                                                  |                                                                                                                                                cGATTGGCAAACCAGCATAGGCGGGTTGCTCCAGCAGAATATCGATGCGTTCGGCATCCAGGGCGTTAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAAc                                                                                                                                              <  1:182544/149‑1 (MQ=255)       gCAAACCAGCATAGGCGGGTTGCTCCAGCAGAATATCGATGCGTTCGGCATCCAGGTCGTTAATGAGGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGGGGCGCAGATAAACATACCCAAAAGAAAACCCTCAc                                                                                                                                        >  1:88302/1‑149 (MQ=255)        cAAACCAGCATAGGCGGGTTGCTCCAGCAGAATATCGATGCGTTCGGCATCCAGGTCGTTAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCAcc                                                                                                                                       <  1:83749/149‑1 (MQ=255)             cAGCATAGGCGGGTTGCTCCAGCAGAATATCGATGCGTTCGGCATCCAGGTCGTTAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAg                                                                                                                                  >  2:116823/1‑149 (MQ=255)                    ggCGGGTTGCTTCAGCAGAATATCGATGCGTTCGGCATCCAGGTCGTTAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGa                                                                                                                           <  1:163318/149‑1 (MQ=255)                          ttGCTCCAGCAGAATATCGATGCGTTCGGCATCCAGGTCGTTAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGttt                                                                                                                     >  1:192765/1‑149 (MQ=255)                               ccAGCAGAATATCGATGCGTTCGGCATCCAGGTCGTTAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGTTTAACTc                                                                                                                <  1:384200/149‑1 (MQ=255)                                 agcagAATATCGATGCGTTCGGCATCCAGGTCGTTAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCt                                                                                                                                           >  1:294986/1‑120 (MQ=255)                                 agcagAATATCGATGCGTTCGGCATCCAGGTCGTTAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCt                                                                                                                                           <  2:294986/120‑1 (MQ=255)                                          gcggggCGTGCGGTATCCAGGTCGTTAGTGATGATAGTTGGTCTGGACAGTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGTTTAACTCACATGATGTTa                                                                                                     <  2:221405/144‑1 (MQ=255)                                                  ttCGGCATCCAGGTCGTTAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGTTTAACTCACATGATGATACTGACTGt                                                                                             >  1:438783/1‑149 (MQ=255)                                                     tgCACCCATGTCGTTAATGAGGGTTGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGTTTAACTCACATGATGATACTGACTGTTGc                                                                                          <  2:266521/148‑1 (MQ=255)                                                       cATCCAGGGCGTTAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGTTTAACTCACATGATGATACTGACTGTTGCTc                                                                                        <  2:371941/149‑1 (MQ=255)                                                         tCCAGGTCGTTAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAACCCCTCACCGTCAGGCGGCGAGGGTTTAACTCACATGATGATACTGACTGTTGCTccc                                                                                      >  1:345333/1‑147 (MQ=255)                                                           cAGGTCGTTAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGACAACCCTCACCGTCAGGCGGCGAGGGTTTAACTCACATGATGATACTTACTGTTGCTCActc                                                                                    >  2:506282/1‑149 (MQ=255)                                                           cAGGTCGTTAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGTTTAACTCACATGATGATACTGACTGTTGCTCActc                                                                                    >  2:199900/1‑149 (MQ=255)                                                              gTCGTTAATGATGATAGTTGGTCTGGACATTTTTCGTCCATGTCTTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGTTTAACTCACATGATGATACTGACTGTTGCTCACTCttt                                                                                 <  1:531757/149‑1 (MQ=255)                                                              gTCGTTAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAAc                                                                                                                                              <  2:306333/88‑1 (MQ=255)                                                              gTCGTTAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAAc                                                                                                                                              >  1:306333/1‑88 (MQ=255)                                                                 gTTAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGTTTAACTCACATGATGATACTGACTGTTGCTCACTCTTTGaa                                                                              <  2:349939/149‑1 (MQ=255)                                                                  ttAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAAcc                                                                                                                                             <  1:366558/85‑1 (MQ=255)                                                                  ttAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAAcc                                                                                                                                             >  2:366558/1‑85 (MQ=255)                                                                     atgatgATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGTTTAACTCACATGATGATACTGACTGTTGCTCACTCTTTGAAGTGa                                                                          >  2:536011/1‑149 (MQ=255)                                                                       gatgatAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGTTTAACTCACATGATGATACTGACTGTTGCTCACTCTTTGAAGTGAtt                                                                        >  1:232402/1‑149 (MQ=255)                                                                        atgatAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGATTAACTCACATGATGATACTGACTGTTCCTCACTCTTTGAAGTGAttt                                                                       >  2:46135/1‑149 (MQ=255)                                                                              gTTGGTCTGGACATTTTTACTCCATGTCTTCTGTGCTGCGAGTGCCGCAGATAAACATACCCAAAAGAAACCCCTCACCGTCAGGCGGCGAGGGTTTAACTCCCATGATGATACTGACTGTTGCTCACTCTTTGAAGTGATTTGCGTca                                                                 <  1:118876/149‑1 (MQ=255)                                                                                      ggACATTTTTACTCCAGGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGTTTAACTCACATGATGATACTGACTGTTGCTCACTCTTTGAAGTGATTTGCGTCACATTCAgg                                                         <  1:69638/149‑1 (MQ=255)                                                                                                  tCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGTTTAACTCACATGATGATACTGACTGTTGCTCACTCTTTGAAGTGATTTGCGTCACATTGAGGGAAGTCCTCAAt                                             >  1:229362/1‑149 (MQ=255)                                                                                                           tcgGTGCTGCGAGTGTCGCAGATAAACATACCCCAAAGAAATCCCTCACCGTCAGGCGGCGAGGGTTTAACTCACATGATGATACTGACTGTTGCTCACTCTTTGAAGTGATTTGCGTCACATTCAGGGAATTCCTCAATGCAGCGCAt                                    <  2:304671/149‑1 (MQ=255)                                                                                                              gtgtTGCGAGTGGCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGTGTACCTCACATGATGATACTGACTGTTGCTCACTCTCTGACGTGATTTGCGTCACAGTCAGGGAATTCCCCGATTCAGCGCATTAt                                 <  2:514890/149‑1 (MQ=255)                                                                                                                            gCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGTTTAACTCACATGATGATACTGACTGTTGCTCACTCTTTGAAGTGATTTGCGTCACATTCAGGGAAGTCCTCAATGCAGCGCATTGTGTATAAATCTTAAt                   >  1:216272/1‑149 (MQ=255)                                                                                                                                aTAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGTTTAACTCACATGATGATACTGACTGTTGCTCACTCTTTGAAGTGATTTGCGTCACATTCAGGGAATTCCTCAATGCAGCGCATTATGTATAAATCTTAATCGcc               >  1:565107/1‑149 (MQ=255)                                                                                                                                             aaagcaaagcCTCACCGTTAGGCGGCGAGGGTTTAACTCACATGATGATCCTGACTGTTGCTCACTCTTTGAAGTGATTTGCGTCACATTCAGGGAATTTCTCAATGCAGCGCATTATGTATAAATCTTAATCGCCTTGGTTTATGGaa  <  1:264294/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                CGATTGGCAAACCAGCATAGGCGGGTTGCTCCAGCAGAATATCGATGCGTTCGGCATCCAGGTCGTTAATGATGATAGTTGGTCTGGACATTTTTACTCCATGTCGTCGGTGCTGCGAGTGTCGCAGATAAACATACCCAAAAGAAAACCCTCACCGTCAGGCGGCGAGGGTTTAACTCACATGATGATACTGACTGTTGCTCACTCTTTGAAGTGATTTGCGTCACATTCAGGGAATTCCTCAATGCAGCGCATTATGTATAAATCTTAATCGCCTTGGTTTATGGAA  >  NC_000913_3_pae_tpiA/643877‑644165

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