New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	281896 =	39 (1.160)	5 (0.160)	5/266	3.6	11.7%	coding (88/1155 nt)	yagA	CP4‑6 prophage; putative DNA‑binding transcriptional regulator
	?	NC_000913_3_pae_tpiA	281923 =	39 (1.230)					coding (61/1155 nt)	yagA	CP4‑6 prophage; putative DNA‑binding transcriptional regulator
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GGGAATGGTGCGGAATGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAG  >  NC_000913_3_pae_tpiA/281776‑282068                                                                                                                                                    |                                                                                                                                                  gggAATGGTGCGGAATGCGCGGGCGGTCCTGGAGACCGGCGGCACCTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGaacaaaa                                                                                                                                                 <  2:480838/150‑1 (MQ=255)        gTGCGGAATGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTc                                                                                                                                          >  2:221794/1‑150 (MQ=255)                 gcgcGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTaa                                                                                                                                 <  2:485766/150‑1 (MQ=255)                  ggcgggcggGGCTGAAGAGCGGCGGCACCTTCCTGAGCCGAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAAt                                                                                                                                <  2:511740/149‑1 (MQ=255)                        cggTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGGTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATg                                                                                                                          <  2:279792/150‑1 (MQ=255)                             cTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTGGGTTGCGGTCGGCGAGGCCACCAAAGCAAACTCAGTAGGTAATGACATGGTAtc                                                                                                                     >  1:137051/1‑150 (MQ=255)                              tGAAGACCGGCGGCACCTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATACCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTAtct                                                                                                                    >  1:512872/1‑150 (MQ=255)                                 aGACCGGCGGCACCTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTAtctctc                                                                                                                 <  2:434447/150‑1 (MQ=255)                                     cggcggCACCTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCAt                                                                                                             >  2:146096/1‑150 (MQ=255)                                           cACCTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAgg                                                                                                       <  1:439197/150‑1 (MQ=255)                                              cTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTaa                                                                                                                                 >  1:480655/1‑121 (MQ=255)                                              cTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTaa                                                                                                                                 <  2:480655/121‑1 (MQ=255)                                               ttCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCAt                                                                                                   <  1:221794/150‑1 (MQ=255)                                                       cccAGCGATGGAGCCACTTGTAGCCGGTGGCAGGCGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATACCAGGGCCTAGGCGACt                                                                                           >  2:473109/1‑150 (MQ=255)                                                               tGGAGCCACTTGTAGCCGGTCGGAGGTGAAGTGGCGAAGGGACGGAATAGGGAACGGATGTTCGCTCCGTCCTGCGATGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCCCTCGCATCCCAGGGCATAAGCGACTCCATAAAc                                                                                   <  2:172184/150‑1 (MQ=255)                                                               gggAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAAc                                                                                   <  2:404842/149‑1 (MQ=255)                                                                       cTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCACAAGCGACTCCTGAAACGGGTTCtt                                                                           <  2:460435/150‑1 (MQ=255)                                                                         tGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGCATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTAt                                                                         <  1:71404/150‑1 (MQ=255)                                                                                      aGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTaa                                                            >  2:454263/1‑150 (MQ=255)                                                                                          gAAATGCCGAAGCGACGGCAGAGGGAACGGATGTCCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAgtgt                                                        <  2:97766/150‑1 (MQ=255)                                                                                              tGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTAc                                                    <  1:146096/150‑1 (MQ=255)                                                                                                  gAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGCCATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATg                                                >  2:308162/1‑150 (MQ=255)                                                                                                      cGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTccc                                            >  1:233286/1‑150 (MQ=255)                                                                                                          ggCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGaa                                        <  2:166071/150‑1 (MQ=255)                                                                                                              gagGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAg                                    >  2:9446/1‑150 (MQ=255)                                                                                                              gagGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAg                                    >  1:396683/1‑150 (MQ=255)                                                                                                                gggAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAgtg                                  <  1:454263/150‑1 (MQ=255)                                                                                                                 ggAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAgtgt                                 >  1:204713/1‑150 (MQ=255)                                                                                                                      ggATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAAc                                                                                   <  2:390634/95‑1 (MQ=255)                                                                                                                      ggATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAAc                                                                                   >  1:390634/1‑95 (MQ=255)                                                                                                                              gCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTcccc                    <  1:319940/150‑1 (MQ=255)                                                                                                                                cccGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCgg                  >  2:589521/1‑150 (MQ=255)                                                                                                                                cccGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCCCAGTTGTTAGTGTCTAAAATGTCCCCGAACAAGTGTTCACTATGTCCCCgg                  >  1:288708/1‑150 (MQ=255)                                                                                                                                  cGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCAt                                                                                       >  1:164023/1‑79 (MQ=255)                                                                                                                                  cGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCAt                                                                                       <  2:164023/79‑1 (MQ=255)                                                                                                                                      cTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTa            <  2:473312/150‑1 (MQ=255)                                                                                                                                        gCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTaca          <  1:9446/150‑1 (MQ=255)                                                                                                                                        gCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTaca          >  2:190529/1‑150 (MQ=255)                                                                                                                                         cGAGGCCAACGAAACGAGCTCAGCACGGAATGACATGGTATCTCTCGCATCCCCGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTacac         <  2:50609/150‑1 (MQ=255)                                                                                                                                           gggCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACAccc       >  1:182090/2‑150 (MQ=255)                                                                                                                                               gAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCaaa   >  2:51642/1‑150 (MQ=255)                                                                                                                                                aacaaaacaaACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAg  <  1:200791/150‑1 (MQ=255)                                                                                                                                                aaaaaaaaaaaCTCAGTACGTACTGACATGGGATCTCATCCAGCCCGGGGCATAAGCGACGCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTCTCTACCTTGGCCCCGAACAAGTGTGCACTATGTCCCCGGACCGTACACCCCAAAg  <  2:214704/147‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                  GGGAATGGTGCGGAATGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAG  >  NC_000913_3_pae_tpiA/281776‑282068

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