New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	1207790 =	36 (0.630)	23 (0.450)	21/254	2.0	39.7%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913_3_pae_tpiA	1209619 =	38 (0.750)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related

TGTATTTCCATCCCCCCCAGAGGCAGATGCTTTTGCGGCATTCCACCCCCACTGAATGATTACTGATTGCTCAATACCACCAATCATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/1207953‑1207790 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGATCTACAACGTAATGCGCTGAACTGTGCAGGATGC  >  NC_000913_3_pae_tpiA/1209619‑1209765                                                                                                                                                                                                                                                                                                                         TGTATTTCCATGCCTCCCAGAGGCAGATGCTTTTGCCGCATTCCACCCCCACTGAATGATTACTGATTGCTCAATACCACCAATCATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTC                                                                                                                                                                    <  2:536676/149‑1     TTTCCATCCCCCCCAGAGGCAGATGCTTTTGCGGCATTCCACCCCCCCTGAATGATTACTGATTGCTCAATACCACCAATCATAACCGGTATAGCTATGAAACCGGGGCGTCCTAATGTAGCCGTTCCCGCATTCAGTTTTGCCCCTTC                                                                                                                                                                >  2:572229/1‑149     TTTCCATCCCCCCCAGAGGCAGATGCTTTTGCGGCATTCCACCCCCACTGAATGATTACTGATTGCTCAATACCACCAATCATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTC                                                                                                                                                                >  1:753721/1‑149     TTTCCATCCCCCCCAGAGGCAGATGCTTTTGCGGCATTCCACCCCCACTGAATGATTACTGATTGCTCAATACCACCAATCATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTC                                                                                                                                                                >  2:356868/1‑149       TCCATCCCCCCCAGAGGCAGATGCTTTTGCGGCATTCCACCCCCACTGACTGATTACTGATTGCTCAAAACAACCAATCATAACTGGTATAGCTATGAACCCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGCGTTTTGCTCCTTCTC                                                                                                                                                              >  2:349935/1‑149       TCCATCCCCCCCAGAGGCAGATGCTTTTGCGGCATTCCACCCCCACTGAATGATTACTGATTGCTCAATACCACCAATCATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTC                                                                                                                                                              <  2:328559/149‑1        CCATCCCCCCCAGAGTCAGAGTCTTTTGCGGCATTCCACCCCTATTGAATGATTACTTATTTCTCAATACCACCAATCATAACCTGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCC                                                                                                                                                             <  2:698299/149‑1               CCCCAGAGGCAGATGCTTTTGCGGCATTCCACCCCCACTGAATGATTACTGATTGCTCACTACCACCAATCATAACCGGTATAGCTATGAGGCGAGGGTTTCCTAATGTAGCCGTTGCTGCATTGCGTTTTGCTCCTTCTCCCCAACCA                                                                                                                                                      >  1:233062/1‑149                 CCAGAGGCAGATGCTTTTGCGGCATTCCACCCCCACTGAATGATTACTGATTGCTCAATACCACCAATCATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAAC                                                                                                                                                    <  1:418647/149‑1                                TTTGCGGCATTCCACCCCCACTGAATGATTACTGATTGCTCAATACCACCAATCATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAA                                                                                                                                     <  1:11309/149‑1                                     GGCATTCCACCCCCACTGAATGATTACTGATAGAACGTCGGTACTAATCATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAAT                                                                                                                                >  1:497160/1‑149                                           CCACCCCCACTGAATGATTACTGATTGCTCAATACCACCAATCATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGCAGAAATAACAAG                                                                                                                          >  1:324541/1‑149                                               CCCCACTGAATGATTACTGATTGCTCAATACCACCAATCATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAA                                                                                                                      >  1:252544/1‑149                                                CCCACTGAATGATTACTGATTGCTCAATACCACCAATCATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAAT                                                                                                                     >  1:983341/1‑149                                                             TACTGATTGCTCAATACCACCAATCATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTG                                                                                                        >  1:431994/1‑149                                                               CTGATTGCTCAATACCACCAGTCATAACCAGTATAGCTATGAAACCGGTGCGTCTTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCT                                                                                                      <  1:870720/149‑1                                                                TGATTGCTCAATACCACCAATCATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTT                                                                                                     >  2:700364/1‑149                                                                  ATTGCTCAATACCACCAATCATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTT                                                                                                   >  2:988447/1‑149                                                                   TTGCTCAATACCACCAATCATAACCGGTATAGCTATGAAACCGGTGCGTACTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAACCAAATGGCATCATTCCTGCTTTTA                                                                                                  >  2:245562/1‑149                                                                    TGCGCAATACCACCAATCATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCCACCCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTAC                                                                                                 <  2:512965/149‑1                                                                         AATACCACCAATCATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTTCTTCTCACAAACCAACGTTTATGAAAATGAAGAAATAAGCAGCAAATGGCATCATTCCTGCGTTTACCAGGG                                                                                            >  1:596467/1‑149                                                                          ATACCACCAATCATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGG                                                                                           >  1:656966/1‑149                                                                                            GGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTGTTCCTTGCTATCGTTTATGAAAATGAAGAAATGACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTG                                                                         >  2:565763/1‑149                                                                                                 AGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTAT                                                                    <  1:176460/149‑1                                                                                                 AGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATAACGAGTCAATAAGAAATTCGAAGCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTAT                                                                    <  1:747023/149‑1                                                                                                               TGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCCTCATTCCTGCTTTTCCCAGGGGGGTTTAACATGCGTTTTGGCTATGTACGCGTCTCAAC                                                      >  1:1010495/1‑149                                                                                                                           TAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCC                                                                                                                                                            <  2:627228/35‑1                                                                                                                           TAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCC                                                                                                                                                            >  1:627228/1‑35                                                                                                                                 TTGCTGCATGGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGA                                    <  2:443464/149‑1                                                                                                                                  TGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGAT                                   <  2:983341/149‑1                                                                                                                                         tcGAGTTTTACTCCATCACCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGTCATCATTCCTGCTTTTACCAGGACAATATGACATGTTTATTGCCTATGTACGCGTATCAACAAATGACCAGAACACAGATCTACAAC                            <  2:622605/147‑1                                                                                                                                                 agaTCCTTCTCCCAAACCAACGGTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACAAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAAACAAGATCTACAACGTAATGCG                    >  2:145204/4‑149                                                                                                                                                    TCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTCGCTATGTACGCGTATCAACAAATGACCAGAACACAGATCTCTAACGTAATGCGCTG                 >  2:65458/1‑149                                                                                                                                                           CCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGATCTACAACGTAATGCGCTGAACTGTG          >  1:75794/1‑149                                                                                                                                                            CCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATTCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAAAACAGATCTACAACGTAATGCGCTTAACTGTGC         >  2:436663/1‑149                                                                                                                                                            CCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGATCTACAACGTAATGCGCTGAACTGTGC         >  1:510059/1‑149                                                                                                                                                            CCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGATCTACAACGTAATGCGCTGAACTGTGC         >  2:273796/1‑149                                                                                                                                                            CCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAAAGACCAGAACACAGATCTACAACGTAATCCGCTGAACTGTGC         >  1:574395/1‑149                                                                                                                                                            CCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCCGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATTTCCACGTAGCAACAAATGACCATAACACACAACTACACCGTAATGCGCTGAACTGTGC         >  2:947269/1‑149                                                                                                                                                            CCAAACCAACGTTTATGAAAAAGAAGAAATAACAACCAAATGGCATCATTCCTGCTTTTACAAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGATCTAAAACGTAATACGCTGAACTGTGC         >  2:875572/1‑149                                                                                                                                                              AAACCAAGGCTGATCAAAATAAAGAAATAACAAGCAAATGGCATCATTCCTGGTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGATCTACAACGTAATGCGCTGAACTGTGCAG       <  2:233250/149‑1                                                                                                                                                                   AACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGATCTACAACGTAATGCGCAGAACTGTGCAGGATGC  <  1:223348/149‑1                                                                                                                                                                   AACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGATATACAACGTAATGCGCTGAACTGTGCAGGATGC  >  1:380321/1‑149                                                                                                                                                                                                                                                                                                                         TGTATTTCCATCCCCCCCAGAGGCAGATGCTTTTGCGGCATTCCACCCCCACTGAATGATTACTGATTGCTCAATACCACCAATCATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/1207953‑1207790 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGATCTACAACGTAATGCGCTGAACTGTGCAGGATGC  >  NC_000913_3_pae_tpiA/1209619‑1209765

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.