New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 3427065	NA (NA)	22 (0.240)	19/222	7.4	NA	intergenic (‑32/+11)	alaU/ileU	tRNA‑Ala/tRNA‑Ile
	?	NC_000913_3_pae_tpiA	= 3427068	NA (NA)					intergenic (‑35/+8)	alaU/ileU	tRNA‑Ala/tRNA‑Ile
Rejected: Coverage evenness skew score above cutoff.

CCTTTGCAGGTACACTCTGAAGTATTTTTTATTTAATCACTACAGAGATGGTGGAGCTATGCGGGATCGAACCGCAGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATTTGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_tpiA/3426910‑3427065 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑caaatttgcACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATACTTCAGAGTGTA  <  NC_000913_3_pae_tpiA/3427068‑3426920                                                                                                                                                                                                                                                                                                                   CCTTTGCAGGTACACTCTGAAGTATTTTTTATTTAATCACTACAGAGATGGTGGAGCTATGCGGGATCGAACCGCAGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAA                                                                                                                                                             >  1:314645/1‑150   TTTGCAGGTACACTCTGAAGTATTTTTTATTTAATCACTACAGAGATGGTGGAGCTATGCGGGATCGAACCGCAGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAAT                                                                                                                                                           >  1:418302/1‑150   TTTGCAGGTACACTCTGAAGTATTTTTTATTTAATCACTACAGAGATGGTGGAGCTATGCGGGATCGAACCGCAGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAAT                                                                                                                                                           >  4:377127/1‑150    TTGCAGGTACACTCTGAAGTATTTTTTATTTAATCACTACAGAGATGGTGGAGCTATGCGGGATCGAACCGCAGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATT                                                                                                                                                          >  2:688873/1‑150    TTGCAGGTACACTCTGAAGTATTTTTTATTTAATCACTACAGAGATGGTGGAGCTATGCGGGATCGAACCGCAGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATT                                                                                                                                                          >  3:56482/1‑150    TTGCAGGTACACTCTGAAGTATTTTTTATTTAATCACTACAGAGATGGTGGAGCTATGCGGGATCGAACCGCAGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATT                                                                                                                                                          <  1:882473/150‑1                   GAAGTATTTTTTATTTAATCACTACAGAGATGGTGGAGCTATGCGGGATCGAACCGCAGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATTTGCACGGCAAATTTG                                                                                                                                           <  3:649197/150‑1                   GAAGTATTTTTTATTTAATCACTACAGAGATGGTGGAGCTATGCGGGATCGAACCGCAGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTCCAAATTTGCACGGCAAATTTG                                                                                                                                           <  1:640159/150‑1                     AGTATTTTTTATTTAATCACTACAGAGATGGTGGAGCTATGCGGGATCGAACCGCAGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATTTGCACGGCAAATTTGAA                                                                                                                                         <  2:1027090/150‑1                     AGTATTTTTTATTTAATCACTACAGAGATGGTGGAGCTATGCGGGATCGAACCGCAGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATTTGCACGGCAAATTTGAA                                                                                                                                         <  1:971022/150‑1                       TATTTTTTATTTAATCACTACAGAGATGGTGGAGCTATGCGGGATCGAACCGCAGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATTTGCACGGCAAATTTGAAGA                                                                                                                                       <  1:116102/150‑1                                       ACTACAGAGATGGTGGAGCTATGCGGGATCGAACCGCAGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATTTG                                                                                                                                                        <  3:629513/117‑1                                       ACTACAGAGATGGTGGAGCTATGCGGGATCGAACCGCAGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATTTG                                                                                                                                                        >  4:629513/1‑117                                                              CGGGATCGAACCGCAGGCCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAAGTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTA                                                                                                             <  4:344229/137‑1                                                              CGGGATCGAACCGCAGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTA                                                                                                             >  3:344229/1‑137                                                                      AACCGCAGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCCAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCC                                                                                        <  1:456464/150‑1                                                                           CAGACCTCCTGCGTGCAAAGCAGGCGCTCGCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTT                                                                                   >  1:669122/1‑150                                                                                    TGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATTTGCACGGCAAATTTGAA                                                                                                                                         >  4:72105/1‑87                                                                                    TGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATTTGCACGGCAAATTTGAA                                                                                                                                         <  3:72105/87‑1                                                                                         GCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCCCTTCAAATTTGCACGGCAAATT                                                                                                                                             >  4:42653/1‑78                                                                                         GCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCCCTTCAAATTTGCACGGCAAATT                                                                                                                                             <  3:42653/78‑1                                                                                           AAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATTTGCACGGCAAATTT                                                                                                                                            >  1:934399/1‑77                                                                                           AAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATTTGCACGGCAAATTT                                                                                                                                            <  2:934399/77‑1                                                                                                     CTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATT                                                                                                                                                          >  1:725564/1‑53                                                                                                     CTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATT                                                                                                                                                          <  2:725564/53‑1                                                                                                                     ATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACC                                         <  1:318953/150‑1                                                                                                                     ATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACC                                         >  2:318953/1‑150                                                                                                                           CCATAACATGTAGTTAAAACCTCTTCAAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGG                                                                                                                  >  2:66488/1‑71                                                                                                                           CCATAACATGTAGTTAAAACCTCTTCAAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGG                                                                                                                  <  1:66488/71‑1                                                                                                                                                  TTCAAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGC                                                                                         >  1:747517/1‑73                                                                                                                                                  TTCAAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGC                                                                                         <  2:747517/73‑1                                                                                                                                                   TCAAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATACTT           >  3:729796/1‑150                                                                                                                                                    CAAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATACTTC          <  4:99620/150‑1                                                                                                                                                    CAAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCA                                                                               <  2:124918/81‑1                                                                                                                                                    CAAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCA                                                                               >  1:124918/1‑81                                                                                                                                                     AAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTG                                                                  <  3:425854/93‑1                                                                                                                                                     AAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTG                                                                  >  4:425854/1‑93                                                                                                                                                     AAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGC                                                                                >  1:10300/1‑79                                                                                                                                                     AAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGC                                                                                <  2:10300/79‑1                                                                                                                                                     AAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGG                                                                                                                  <  2:448830/45‑1                                                                                                                                                     AAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGG                                                                                                                  >  1:448830/1‑45                                                                                                                                                      AATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATAC             >  2:1265208/1‑145                                                                                                                                                      AATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATAC             <  1:1265208/145‑1                                                                                                                                                      AATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGA                                                          >  2:1227882/1‑100                                                                                                                                                      AATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGA                                                          <  1:1227882/100‑1                                                                                                                                                       ATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATACTTCAGA       <  3:622779/150‑1                                                                                                                                                       ATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATACTTCAGA       <  3:726931/150‑1                                                                                                                                                        TTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGG                                                                                                 <  3:413943/59‑1                                                                                                                                                        TTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGG                                                                                                 >  4:413943/1‑59                                                                                                                                                         TTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATACTTCAGAGT     >  1:777052/1‑150                                                                                                                                                            CACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATACTTCAGAGTGTA  >  1:936876/1‑150                                                                                                                                                            CACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATACTTC          >  4:152807/1‑142                                                                                                                                                            CACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATACTTC          <  3:152807/142‑1                                                                                                                                                                                                                                                                                                                   CCTTTGCAGGTACACTCTGAAGTATTTTTTATTTAATCACTACAGAGATGGTGGAGCTATGCGGGATCGAACCGCAGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTATAGCCCCATAACATGTAGTTAAAACCTCTTCAAATTTGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_tpiA/3426910‑3427065 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑caaatttgcACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATACTTCAGAGTGTA  <  NC_000913_3_pae_tpiA/3427068‑3426920

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.