New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	164559 =	47 (1.210)	4 (0.110)	4/268	5.1	9.6%	intergenic (+25/‑171)	hrpB/mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
	?	NC_000913_3_pae_tpiA	289255 =	31 (0.850)					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.

GACTTCTGGAAAGGAGCGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTT  >  NC_000913_3_pae_tpiA/164412‑164702                                                                                                                                                    |                                                                                                                                                 gACTTCTGGAAAGGAGGGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGGCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTgg                                                                                                                                                 <  1:143398/149‑1 (MQ=255)    ttCTGGAAAGGAGCGTACCGTGAGGTGCAAAAAGCAATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGgag                                                                                                                                              >  2:634369/1‑149 (MQ=255)    ttCTGGAAAGGAGCGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAACGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGgag                                                                                                                                              >  1:181302/1‑149 (MQ=255)      cTGGAAAGGAGCGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTTAGGTTGGTTTTCTCCCTCTCCCTGTGGGagag                                                                                                                                            >  1:26183/1‑149 (MQ=255)       tGGAAAGGAGCGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAgg                                                                                                                                           >  1:73280/1‑149 (MQ=255)          aaaGGAGCGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCTTAAGGTTGGTTTTCGCCCTCTCCCACAGGGAGAgggag                                                                                                                                        <  2:147668/149‑3 (MQ=255)          aaaGGAGCGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGCTTTTCTCCCTCTCCCTGTGGGAGAGGGcc                                                                                                                                        >  1:586408/1‑149 (MQ=255)           aaGGAGCGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGCGCCg                                                                                                                                       >  1:292327/1‑149 (MQ=255)                 cGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAGAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGa                                                                                                                                 <  1:450306/149‑1 (MQ=255)                     ccGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGGCGGGGTGGGGGc                                                                                                                             >  1:135140/1‑149 (MQ=255)                      cGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGCACGGTTGCCTCTCTGCCTCTCCCTGTGGGAGAAGGCCGGGGTGAGGGCa                                                                                                                            >  1:300047/1‑149 (MQ=255)                        tGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGCCGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATc                                                                                                                          >  2:295237/1‑149 (MQ=255)                                aaaaaGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCa                                                                                                                 >  2:227680/1‑149 (MQ=255)                                        aTGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTtcacc                                                                                                         <  2:181302/149‑1 (MQ=255)                                          gAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGAACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTtcaccct                                                                                                       >  2:210954/1‑149 (MQ=255)                                           aaaGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTtcaccctc                                                                                                      >  1:370289/1‑149 (MQ=255)                                              gggCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGAGCCGGGGTGAGGGCATCAGCGC‑GCACGTtcaccctcacc                                                                                                   >  1:284146/1‑149 (MQ=255)                                                  gTTATCGTAAACACGTCGCGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTaa                                                                                               <  2:241966/149‑1 (MQ=38)                                                       cccAAACATGTCTGGGCGGACGTCCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGCGTGA‑AAAAGCAGATCGGTAGTTTCACCCTCACCCTAACCctc                                                                                          <  2:490899/149‑1 (MQ=255)                                                        ccAAACATGTCTGGCCGGGCGACCCGGCAAATACTGAAAAGAAGCGACGGACGAAAACGTGATCGAAACGTTGTTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCctct                                                                                         >  2:656008/1‑149 (MQ=25)                                                           aaCATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTccc                                                                                      >  2:146170/1‑149 (MQ=255)                                                                 tCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAgg                                                                                >  1:228963/1‑149 (MQ=255)                                                                 tCTGGCCGGACGACCCGGCAAATACAGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTATCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGTCATCCGCGC‑GCACGTTCACCCCCACCCTCACCCTCTcccccccgg                                                                                >  2:51158/1‑143 (MQ=38)                                                                   tGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCCCTCCCCCAAGGga                                                                              >  2:416390/1‑149 (MQ=255)                                                                     gCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCctct                                                                                         >  1:109361/1‑136 (MQ=255)                                                                     gCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCctct                                                                                         <  2:109361/136‑1 (MQ=255)                                                                      ccGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGagag                                                                           <  2:370289/149‑1 (MQ=255)                                                                       cGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAgg                                                                          <  2:586408/149‑1 (MQ=255)                                                                       cGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAgg                                                                          <  1:227680/149‑1 (MQ=255)                                                                               ccGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGGTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTACCCCTCACCCTAACCCTCTCCCTCAAGGGAGGGGAGACCGAt                                                                  >  2:407298/1‑149 (MQ=38)                                                                                  gCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGa                                                               <  1:611630/149‑1 (MQ=255)                                                                                             aCCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAAtttt                                                    >  1:184090/1‑149 (MQ=255)                                                                                                 acgcgacgGAGGATAAAGTATTCGGAAGGTTGGTTTTCGCCCGCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTgaga                                                <  2:328236/149‑1 (MQ=38)                                                                                                  cgcgacgGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCAAGAACAAATTTTgagag                                               >  1:170537/1‑149 (MQ=255)                                                                                                            gAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGACTTAGATAGGGCAGCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCAAAAATTTTGAGAGATAtcttctt                                     >  2:624710/1‑149 (MQ=255)                                                                                                                  gTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGTAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGTGGGGACCGATCGCGCACAAATCTTGAGAGATATCTTCTTCTGTCt                               <  1:541343/149‑1 (MQ=255)                                                                                                                    aTTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTg                             <  1:146170/149‑1 (MQ=255)                                                                                                                       cGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCGCAAATTTTGAGAGATATCTTCTTCTGTCTTGTaa                          <  2:541688/149‑1 (MQ=255)                                                                                                                         tAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGTGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATAGCTTCTTCTGTCTTGTAACa                        <  1:546656/149‑1 (MQ=255)                                                                                                                             gttggttTTCTCCCTCTCCCTGGCGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACagaag                    <  1:146692/149‑1 (MQ=255)                                                                                                                                ggttTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAAc                 >  1:6397/1‑149 (MQ=255)                                                                                                                                 gttTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCCGCGC‑GCACGTTTACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACa                >  1:643763/1‑149 (MQ=255)                                                                                                                                  ttttCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAg               >  1:75061/1‑149 (MQ=255)                                                                                                                                        ccctctcccaCAGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACag                       <  1:358207/135‑1 (MQ=255)                                                                                                                                          ctctccctGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCGTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCgg       >  1:513250/1‑149 (MQ=255)                                                                                                                                          ctctccctGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGCAAATCgg       >  2:586606/1‑149 (MQ=255)                                                                                                                                          ctctccctGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCgg       <  2:6397/149‑1 (MQ=255)                                                                                                                                               cctGTCGGAGAGGGAGGGGGTGAGGGCAGCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACCAATTTTGAGAGATGTCTTCTTCTGTCTTGTAACAGAAGAACAGAGAATCGGGCgtt  >  2:593119/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                 GACTTCTGGAAAGGAGCGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGC‑GCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTT  >  NC_000913_3_pae_tpiA/164412‑164702

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.