New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	127837 =	148 (0.730)	8 (0.050)	6/138	NT	5.7%	intergenic (+57/+272)	lctP_1/spa	L‑lactate permease/Immunoglobulin G‑binding protein A
	?	USA300TCH1516_ALE	127883 =	138 (0.790)					intergenic (+103/+226)	lctP_1/spa	L‑lactate permease/Immunoglobulin G‑binding protein A

AACGCCTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/127937‑127837 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ctagttcgattTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGTAAAATAAAAA  >  USA300TCH1516_ALE/127883‑127972                                                                                                                                                                                                 AACGCCTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTAC                                                                                                      <  2:83016/91‑1  tCGCCTCAACACTCTCTACTCTGATGACATAGATGGCATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACT                                                                                                     <  2:3912461/90‑1  ACGCCTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACT                                                                                                     <  1:121954/91‑1  ACGCCTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACT                                                                                                     <  1:2259573/91‑1   CGCCTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTA                                                                                                    <  1:17431/91‑1   CGCCTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTA                                                                                                    <  1:1755320/91‑1   CGCCTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTA                                                                                                    >  2:1629916/1‑91    GCCTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAG                                                                                                   >  2:3272030/1‑91    GCCTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAG                                                                                                   >  2:1460027/1‑91    GCCTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAG                                                                                                   >  1:33150/1‑91     CCTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACTAGATGCTCATTGCATTTCGTACTAGT                                                                                                  <  2:2245239/91‑1     CCTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGT                                                                                                  <  2:1466089/91‑1     CCTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGT                                                                                                  <  2:3818468/91‑1     CCTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGT                                                                                                  <  2:3818110/91‑1     CCTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGT                                                                                                  <  2:1466075/91‑1     CCTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGT                                                                                                  <  1:480504/91‑1      CTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGCTGCTCATTGCATTTCGTACTAGTT                                                                                                 >  2:3359143/1‑91      CTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTT                                                                                                 <  2:769298/91‑1      CTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTT                                                                                                 >  2:3693095/1‑91      CTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTT                                                                                                 <  2:1733317/91‑1      CTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTT                                                                                                 >  2:1848690/1‑91      CTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTT                                                                                                 >  2:1848748/1‑91       TCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTC                                                                                                >  2:348180/1‑91       TCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTC                                                                                                >  2:347985/1‑91       TCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTC                                                                                                >  2:1156468/1‑91        CAACACTTTCTGCTCTGATTACACATATGACATTTTTAGGCATTAAAAAATCGAACTAGCCAAGATGCTCATTGCATTTCGTACTAGTTCG                                                                                               <  2:3023198/91‑1         AACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGA                                                                                              >  2:1654691/1‑91         AACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGA                                                                                              <  2:905419/91‑1         AACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGA                                                                                              >  2:1654756/1‑91         AACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGA                                                                                              <  2:1865536/91‑1         AACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGA                                                                                              <  1:2490953/91‑1         AACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGA                                                                                              >  2:2941920/1‑91         AACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGA                                                                                              >  2:2941939/1‑91         AACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGA                                                                                              >  1:1930367/1‑91         AACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGA                                                                                              >  1:3389881/1‑91          ACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGAT                                                                                             >  2:3433405/1‑91          ACACTTTCTACTCTGATTACATATATGACATTTTTAGGAATTAAAAAATCGAACTAGACAAAATGATCATTGCATTTATTATTAGCTCGAT                                                                                             >  2:18266/1‑91           CACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGATT                                                                                            >  1:2913792/1‑91             CTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGATTTT                                                                                          >  1:1464965/1‑91                                                         ATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGATGTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGT                                              >  2:3890082/1‑91                                                          TCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTT                                             >  1:3114909/1‑91                                                              ACTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGG                                         >  2:3633480/1‑91                                                               CTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGC                                        >  1:2507258/1‑91                                                               CTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGC                                        >  1:2507273/1‑91                                                                  gatAAGATGCTCATTGCATTTCGTACTAGTTCGATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTT                                     >  2:1040247/4‑91                                                                  GACAAGATGCTCATTGCATTTCGTACTAGTTCGATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTT                                     >  2:1069369/1‑91                                                                   ACAAGATGCTCATTGCATTTCGTACTAGTTCGATTTTTTATTGCTTTAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTT                                    >  2:1617329/1‑91                                                                                           CTAGTTCGATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGT            <  1:1172385/91‑1                                                                                           CTAGTTCGATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGT            >  2:1745299/1‑91                                                                                            TAGTTCGATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGTA           >  1:339157/1‑91                                                                                            TAGTTCGATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGTA           >  2:2296917/1‑91                                                                                             AGTTCGATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGTAA          <  1:2336295/91‑1                                                                                              GTTCGATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGTAAA         <  2:3203907/91‑1                                                                                              GTTCGATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGTAAA         <  1:1405734/91‑1                                                                                              GTTCGATTTTTGAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTATTTAGAAAAGTAAGTAAA         <  2:3314415/91‑1                                                                                               TTCGATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGTAAAA        <  1:2887257/91‑1                                                                                               TTCGATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGTAAAA        <  1:95406/91‑1                                                                                               TTCGATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGTAAAA        <  1:95442/91‑1                                                                                                TCGATTTTTTAATGCCTAAAAATGTCATATATGTAATGAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGAAAAAT       >  1:3681111/1‑91                                                                                                TCGATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGTAAAAT       >  1:2477928/1‑91                                                                                                 CGATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAATAAAATA      <  2:503224/91‑1                                                                                                  GATTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGTAAAATAA     <  1:3899323/91‑1                                                                                                    TTTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGTAAAATAAAA   >  1:2973871/1‑91                                                                                                    TTTCTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGTAAAATAAAA   <  1:3190979/91‑1                                                                                                    TTTATTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGTAAAATAAAA   <  1:3191012/91‑1                                                                                                     TTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGTAAAATAAAAA  >  2:1427759/1‑91                                                                                                                                                                                                 AACGCCTCAACACTTTCTACTCTGATTACATATATGACATTTTTAGGCATTAAAAAATCGAACTAGACAAGATGCTCATTGCATTTCGTACTAGTTCGATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/127937‑127837 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ctagttcgattTTTTAATGCCTAAAAATGTCATATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTTCAGAAGTTGTTTAGAAAAGTAAGTAAAATAAAAA  >  USA300TCH1516_ALE/127883‑127972

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