New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	164559 =	113 (1.120)	21 (0.220)	19/222	7.4	18.7%	intergenic (+25/‑171)	hrpB/mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
	?	NC_000913_3_pae_tpiA	289255 =	78 (0.830)					intergenic (‑93/+46)	yagI/argF	CP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

ATATTCAGGCGCAAAAGCCCGATTTTCTGTTCTTCTGTTACAAGACAGAAGAAGATATCTCTCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/164715‑164559 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccctctcccTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTC  >  NC_000913_3_pae_tpiA/289255‑289403                                                                                                                                                                                                                                                                                                                    ATATTCAGGCGCAAAAGCCCGATTTTCTGTTCTTCTGTTACAAGACAGAAGAAGATATCTCTCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCC                                                                                                                                                              >  2:321505/1‑150       AGGCGCAAAAGCCCGATTTTCTGTTCTTCTGTTACAAGACAGAAGAAGATATCTCTCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCC                                                                                                                                                        <  1:321505/150‑1        GGCGCAAAAGCCCGATTTTCTGTTCTTCTGTTACAAGACAGAAGAAGATATCTCTCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCC                                                                                                                                                       >  3:506464/1‑150             AAAAGCCCGATTTTCTGTTCTTCTGTTACAAGACAGAAGAAGATATCTCTCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCCTGTGG                                                                                                                                                  <  2:1164839/150‑1                    CGATTTTCTGTTCTTCTGTTACAAGACAGAAGAAGATATCTCTCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGACGGTTAGGGTGAGGGTGAACGTGCGCGCTCATGCCCTCACCCCGGCCCTCTCCCTGTGGGAGAGGG                                                                                                                                           <  2:1028394/150‑1                         TTCTGTTCTTCTGTTACAAGACAGAAGAAGATATCTCTCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCCTGTGGGAGAGGGCCGGG                                                                                                                                      <  4:506464/150‑1                              TTCTTCTGTTACAAGACAGAAGAAGATATCTCTCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAG                                                                                                                                 <  1:954761/150‑1                                                GAAGAAGATATCTCTCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCCTGTGGGAGAGGGCCGG                                                                                                                                       >  1:285837/1‑126                                                GAAGAAGATATCTCTCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCCTGTGGGAGAGGGCCGG                                                                                                                                       <  2:285837/126‑1                                                   GAAGATATCTCTCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCC                                                                                                                                                              >  2:768072/1‑100                                                   GAAGATATCTCTCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCC                                                                                                                                                              <  1:768072/100‑1                                                              TCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGG                                                                                                                                <  3:292983/119‑1                                                              TCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGG                                                                                                                                >  4:292983/1‑119                                                                      TGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCCTGTGGGAGAGG                                                                                                                                            <  1:1142222/99‑1                                                                      TGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCCTGTGGGAGAGG                                                                                                                                            >  2:1142222/1‑99                                                                                     CCCTCTCCCTCAAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCT                                                                                                                                                          <  1:509959/70‑1                                                                                     CCCTCTCCCTCAAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCT                                                                                                                                                          >  2:509959/1‑70                                                                                       CTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCA                                                                                                                             >  1:163563/1‑97                                                                                       CTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCA                                                                                                                             <  2:163563/97‑1                                                                                         CTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCT                                                                                                                                                          <  1:1234231/66‑1                                                                                         CTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCT                                                                                                                                                          >  2:1234231/1‑66                                                                                               caAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTC                                                                                                                                                         <  1:1082503/59‑1                                                                                               caAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTC                                                                                                                                                         >  2:1082503/3‑61                                                                                                         GGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCCTGTGGGAGAGGGCCGGG                                                                                                                                      >  2:551849/1‑70                                                                                                         GGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCCTGTGGGAGAGGGCCGGG                                                                                                                                      <  1:551849/70‑1                                                                                                                                            TCACCCCGGCCCTCTCCCACAGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCC                                                  <  4:574327/119‑1                                                                                                                                            TCACCCCGGCCCTCTCCCACAGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCC                                                  >  3:574327/1‑119                                                                                                                                                CCCGGCCCTCTCCCACAGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAA               >  2:3250/1‑150                                                                                                                                                 CCGGCCCTCTCCCACAGGGAGAGGGACGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACCCCCCAAGCGTTGTCAACATCGCCGCCTTAATCGTATGCATCCGGGTTTCCGGCTGGTCGAACACGATGCTCGCCGCCGACTCAAAC              >  1:588520/1‑150                                                                                                                                                  CGGCCCTCTCCCACAGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACCCCCCAAGCGTTGCCATCATCACCCCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGCCTCAAACc             >  4:298745/1‑149                                                                                                                                                  CGGCCCTCTCCCACAGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAAT                                                                                                        >  4:448103/1‑59                                                                                                                                                  CGGCCCTCTCCCACAGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAAT                                                                                                        <  3:448103/59‑1                                                                                                                                                     CCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCT          >  1:632626/1‑150                                                                                                                                                     CCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCT          >  1:631937/1‑150                                                                                                                                                      CCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTC                  <  2:238950/141‑1                                                                                                                                                      CCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTC                  >  1:238950/1‑141                                                                                                                                                      CCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAAT                                                                                                        <  2:1019524/55‑1                                                                                                                                                      CCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAAT                                                                                                        >  1:1019524/1‑55                                                                                                                                                       CTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCG        <  1:408204/150‑1                                                                                                                                                       CTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCG        >  2:717583/1‑150                                                                                                                                                       CTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTAT                                                                <  4:351604/94‑1                                                                                                                                                       CTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTAT                                                                >  3:351604/1‑94                                                                                                                                                        TCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCC                                                                                      <  3:511939/71‑1                                                                                                                                                        TCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCC                                                                                      >  4:511939/1‑71                                                                                                                                                         CTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTC      <  1:1194127/150‑1                                                                                                                                                          TCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCC     <  2:632626/150‑1                                                                                                                                                          TCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCC     <  2:631937/150‑1                                                                                                                                                             CTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGC                                                >  4:211201/1‑104                                                                                                                                                             CTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGC                                                <  3:211201/104‑1                                                                                                                                                             CTGTGGAAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTC  >  4:604677/1‑150                                                                                                                                                                                                                                                                                                                    ATATTCAGGCGCAAAAGCCCGATTTTCTGTTCTTCTGTTACAAGACAGAAGAAGATATCTCTCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/164715‑164559 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccctctcccTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTC  >  NC_000913_3_pae_tpiA/289255‑289403

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.