New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_hsa_tpiA	2068389 =	87 (1.040)	21 (0.290)	18/218	5.3	24.8%	pseudogene (31/159 nt)	yoeH	pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related
	?	NC_000913_3_hsa_tpiA	2068430 =	53 (0.740)					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.

CATCTTCATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_hsa_tpiA/2068549‑2068389 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagagtgcggtccgtggaTACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTATAGATATATGAGAACA  >  NC_000913_3_hsa_tpiA/2068430‑2068575                                                                                                                                                                                                                                                                                                                     CATCTTCATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTG                                                                                                                                                               <  2:491364/150‑1  ATCTTCATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGC                                                                                                                                                              >  2:227296/1‑150   TCTTCATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCG                                                                                                                                                             >  2:259400/1‑150   TCTTCATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCG                                                                                                                                                             <  1:154923/150‑1   TCTTCATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCG                                                                                                                                                             <  1:917346/150‑1        ATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCG                                                                                                                                                        >  1:985533/1‑150         TAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGT                                                                                                                                                       >  1:117439/1‑150         TAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGT                                                                                                                                                       <  2:777622/150‑1                      TCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGA                                                                                                                                          <  1:643070/150‑1                         AACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGA                                                                                                                                                                  <  1:450000/123‑1                         AACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGA                                                                                                                                                                  >  2:450000/1‑123                                                                                          TCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCC                                                                                                                                                         >  1:520713/1‑67                                                                                          TCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCC                                                                                                                                                         <  2:520713/67‑1                                                                                                TCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTC                                                                                              >  3:154909/1‑120                                                                                                TCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTC                                                                                              <  4:154909/120‑1                                                                                                    GTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTT                                                                                                   >  3:582641/1‑111                                                                                                    GTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTT                                                                                                   <  4:582641/111‑1                                                                                                        GTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAA                                                        >  3:616843/1‑150                                                                                                            GTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATC                                                                                    >  1:756036/1‑118                                                                                                            GTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATC                                                                                    <  2:756036/118‑1                                                                                                                                  CGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGA                              >  2:761388/1‑150                                                                                                                                  CGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTT                                                   >  3:514317/1‑129                                                                                                                                  CGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTT                                                   <  4:514317/129‑1                                                                                                                                  CGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGG                                                               >  1:740519/1‑117                                                                                                                                  CGCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGG                                                               <  2:740519/117‑1                                                                                                                                   GCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGA                                                                                                                           >  1:145784/1‑56                                                                                                                                   GCACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGA                                                                                                                           <  2:145784/56‑1                                                                                                                                    CACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTAC                                          >  3:472784/1‑136                                                                                                                                    CACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTAC                                          <  4:472784/136‑1                                                                                                                                     ACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTT                                                   <  2:4094/126‑1                                                                                                                                     ACTCTTGACATAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTT                                                   >  1:4094/1‑126                                                                                                                                               TAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAA                                                                          <  3:491754/93‑1                                                                                                                                               TAAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAA                                                                          >  4:491754/1‑93                                                                                                                                                AAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGA                                                 >  2:200005/1‑117                                                                                                                                                AAGAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGA                                                 <  1:200005/117‑1                                                                                                                                                  GAGTGCGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTATAGA              <  2:643070/150‑1                                                                                                                                                       CGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTAT                 >  1:415814/1‑142                                                                                                                                                       CGGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTAT                 <  2:415814/142‑1                                                                                                                                                        GGTCCGTGGATACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTATAGATATATG        >  4:46468/1‑150                                                                                                                                                              TGGATACAACCAGAGAACGACTGACACGAATTAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATAAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTATAGATATATGAGAACA  <  2:917346/150‑1                                                                                                                                                                                                                                                                                                                     CATCTTCATAAATTGTAAATATCAAACATTTTTGACCTTAATCATGTTTTTTGATAGATATTTTACGACTGAACATATCCGTCGTTTCCTCTGACTCGTGTCAGTCGGTCTCTGGTTGTATCCACGGACCGCACTCTTGACATAAGAGTGCGGTCCGTGGA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_hsa_tpiA/2068549‑2068389 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagagtgcggtccgtggaTACAACCAGAGACCGACTGACACGAGTCAGAGGAAACGACGGATATGTTCAGTCGTAAAATATCTATCAAAAAACATGATTAAGGTCAAAAATGTTTGATATTTACAATTTATGAAGATGACAATAATTATAGATATATGAGAACA  >  NC_000913_3_hsa_tpiA/2068430‑2068575

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