New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	2068389 =	162 (1.080)	26 (0.200)	19/218	12.1	18.0%	pseudogene (31/159 nt)	yoeH	pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related
	?	NC_000913_3_pae_tpiA	2068430 =	98 (0.760)					intergenic (‑11/‑205)	yoeH/yoeA	pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related/CP4‑44 prophage; putative disrupted hemin or colicin receptor;Phage or Prophage Related; interrupted by IS2 and C‑terminal deletion
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TATTGTCATCTTCATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/2068555‑2068389 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagagtgcggtccgtggaTACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTATAGATATATGAGAACATAA  >  NC_000913_3_pae_tpiA/2068430‑2068578                                                                                                                                                                                                                                                                                                                              TATTGTCATCTTCATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATA                                                                                                                                                                        >  1:1394996/1‑150  ATTGTCATCTTCATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAA                                                                                                                                                                       <  2:1394996/150‑1      TCATCTTCATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGT                                                                                                                                                                   >  1:204109/1‑150      TCATCTTCATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGT                                                                                                                                                                   >  3:1056692/1‑150        ATCTTCATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGC                                                                                                                                                                 >  1:1429114/1‑150         TCTTCATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCG                                                                                                                                                                <  2:1429114/150‑1           TTCATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGT                                                                                                                                                              >  1:83127/1‑150            TCATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTC                                                                                                                                                             >  2:511213/1‑150              ATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCG                                                                                                                                                           >  1:1308877/1‑150               TAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGT                                                                                                                                                          >  4:33528/1‑150                          TATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCG                                                                                                                                                                >  1:1136867/1‑133                          TATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCG                                                                                                                                                                <  2:1136867/133‑1                            TCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGA                                                                                                                                             <  3:33528/150‑1                                                            ATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGCCTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGA                                                                                                                        <  1:1722966/139‑1                                                            ATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGA                                                                                                                        >  2:1722966/1‑139                                                               GATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTG                                                                                                                                                                  <  1:667553/94‑1                                                               GATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTG                                                                                                                                                                  >  2:667553/1‑94                                                                                             TCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGAAACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAAC                                                                            >  3:994851/1‑150                                                                                                          GTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAATGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCA                                                               >  1:935907/1‑150                                                                                                                   TCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTT                                                      >  3:107472/1‑150                                                                                                                   TCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTT                                                      <  4:107472/150‑1                                                                                                                      CTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGAT                                                   >  1:473447/1‑150                                                                                                                                CCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATT                                         >  4:71280/1‑150                                                                                                                                CCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATT                                         <  2:473447/150‑1                                                                                                                                 CACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTT                                        >  1:1011077/1‑150                                                                                                                                 CACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAG                                                                   >  4:1074221/1‑123                                                                                                                                 CACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAG                                                                   <  3:1074221/123‑1                                                                                                                                  ACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGAT                                                                                                           >  4:770578/1‑82                                                                                                                                  ACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGAT                                                                                                           <  3:770578/82‑1                                                                                                                                     GACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTT                                                      >  1:1217255/1‑132                                                                                                                                     GACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTT                                                      <  2:1217255/132‑1                                                                                                                                     GACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGA                                                                                                                        >  1:793393/1‑66                                                                                                                                     GACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGA                                                                                                                        <  2:793393/66‑1                                                                                                                                        CGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGA                                 >  2:886934/1‑150                                                                                                                                        CGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTT                                                      <  4:182053/129‑1                                                                                                                                        CGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTT                                                      >  3:182053/1‑129                                                                                                                                        CGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAA                                                                             >  2:63348/1‑106                                                                                                                                        CGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAA                                                                             <  1:63348/106‑1                                                                                                                                           ACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACAC                                                                                                                                <  2:428874/52‑1                                                                                                                                           ACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACAC                                                                                                                                >  1:428874/1‑52                                                                                                                                                      AAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTATA                   <  2:290012/150‑1                                                                                                                                                      AAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTATA                   >  2:281034/1‑150                                                                                                                                                      AAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTT                                                      <  2:805520/115‑1                                                                                                                                                      AAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTT                                                      >  1:805520/1‑115                                                                                                                                                      AAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAA                                                                                           <  1:1437602/78‑1                                                                                                                                                      AAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAA                                                                                           >  2:1437602/1‑78                                                                                                                                                       AGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTATAG                  <  4:1070985/150‑1                                                                                                                                                           TGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTATAGATAT              <  2:1205578/150‑1                                                                                                                                                           TGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAA                                           >  3:628257/1‑121                                                                                                                                                           TGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAA                                           <  4:628257/121‑1                                                                                                                                                           TGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGGCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACACTAATTATAGATAT              >  2:1594096/1‑150                                                                                                                                                             CGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTATAGATATAT            >  4:391422/1‑150                                                                                                                                                              GGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTATAGATATATG           >  2:1336771/1‑150                                                                                                                                                               GTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTATAGATATATGA          >  3:861479/1‑150                                                                                                                                                                TCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTATAGATATATGAG         >  3:742799/1‑150                                                                                                                                                                 CCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTATAGATATATGAGA        >  2:503313/1‑150                                                                                                                                                                 CCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTATAGATATATGAGA        >  4:762533/1‑150                                                                                                                                                                       ATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTATAGATATATGAGAACATAA  >  3:211031/1‑150                                                                                                                                                                                                                                                                                                                              TATTGTCATCTTCATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/2068555‑2068389 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagagtgcggtccgtggaTACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTATAGATATATGAGAACATAA  >  NC_000913_3_pae_tpiA/2068430‑2068578

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