New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1911930 =	183 (0.900)	8 (0.040)	3/142	NT	6.4%	coding (52/609 nt)	USA300HOU_RS15290	hypothetical protein
	?	USA300TCH1516_ALE	2318846 =	73 (0.400)					coding (226/300 nt)	USA300HOU_RS12765	hypothetical protein

GTTATTAGGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAATAAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1912028‑1911930 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tttaataaa‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAATATGAC  >  USA300TCH1516_ALE/2318846‑2318935                                                                                                                                                                                                GTTATTAGGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCAAGTTTTATCT                                                                                                     <  2:1442569/91‑1  TTATTAGGACATATAGATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTT                                                                                                    <  2:788503/91‑1  TTATTAGGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTT                                                                                                    >  1:1091120/1‑91   TATTAGGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTT                                                                                                   <  1:1035942/91‑1   TATTAGGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTT                                                                                                   >  1:2307702/1‑91    ATTAGGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTA                                                                                                  <  2:2106379/91‑1    ATTAGGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTA                                                                                                  <  2:2105820/91‑1     TTAGGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAA                                                                                                 <  2:2288231/91‑1     TTAGGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTCAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAA                                                                                                 >  1:3137157/1‑91     TTAGGACATATAAATTCATCATTAAGTTCGTCATATGTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAA                                                                                                 <  2:882075/91‑1      TAGGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAAT                                                                                                >  1:3056010/1‑91      TAGGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAAT                                                                                                >  1:3253197/1‑91      TAGGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAAT                                                                                                >  2:296144/1‑91      TAGGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAAT                                                                                                <  1:623014/91‑1      TAGGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTCTTAAACTTTCTAGTTTTATCTTTAAT                                                                                                >  2:1847693/1‑91       AGGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAATA                                                                                               <  1:3611533/91‑1        GGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAATAA                                                                                              <  2:2272914/91‑1        GGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAATAA                                                                                              <  1:3834174/91‑1        GGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAATAA                                                                                              <  1:3834198/91‑1                         ATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAATAAA‑ACGCCACTTATTACGT                                                                            <  1:3021261/91‑1                                    CATATTTCCAATTTTGAGTGTTGAAAATGCCACTTTTAAACTTTCTAGTTTTATCTTTAATAAACACGCCACTTATTACGTATGGCATGTT                                                                  <  2:3950650/91‑1                                         TTCCAATTTTTAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAATAAA‑ACGCCACTGATTACGTATGGCATGTTTATTAA                                                            <  2:2634318/91‑1                                         TTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAATAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAA                                                            <  2:2634075/91‑1                                         TTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAATAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAA                                                            <  2:3108974/91‑1                                           CCAATTTTAAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAATAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAG                                                          <  1:3381802/91‑1                                             AATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAATAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGAT                                                        <  1:721536/91‑1                                               TTTTGAGTGTTGAAAATGCCACTTTTAAACTTACTAGTTTTATCTTTAATAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAA                                                      <  1:3356720/91‑1                                                                                            TTAATAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAA         >  2:2011315/1‑91                                                                                             TAATAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAA        >  1:677531/1‑91                                                                                             TAATAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAA        >  1:677716/1‑91                                                                                             TAATAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAA        <  1:692399/91‑1                                                                                             TAATAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAA        >  1:3630227/1‑91                                                                                             TAATAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAA        <  1:693901/91‑1                                                                                              AATAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAAT       <  2:1351246/91‑1                                                                                              AATAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAAT       >  2:2882913/1‑91                                                                                              AATAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAAT       <  2:2500234/91‑1                                                                                              AATAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAAT       >  2:2880407/1‑91                                                                                              AATAAA‑ACGCCACGTATTACGTATGGCATGGTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAAT       <  2:3934182/91‑1                                                                                               ATAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAATA      >  2:1232952/1‑91                                                                                               ATAAA‑ACGCCACTTATTACGTATGGCATGTTCATTAAAGATCAAACTAGAAAGTTTACAAGTGACATGATCAACACTTAAAATTGGAAATA      >  2:3006387/1‑91                                                                                                TAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAATAT     >  2:2367067/1‑91                                                                                                TAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAATAT     >  2:2367108/1‑91                                                                                                TAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAATAT     >  2:1055446/1‑91                                                                                                TAAA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAATAT     >  2:1054895/1‑91                                                                                                  AA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAATATGA   <  2:2805424/91‑1                                                                                                  AA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAATATGA   >  2:2158085/1‑91                                                                                                  AA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAATATGA   >  2:2157815/1‑91                                                                                                  AA‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAATATGA   >  2:1448755/1‑91                                                                                                   A‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAATATGAC  >  1:833337/1‑91                                                                                                   A‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAATATGAC  >  1:119711/1‑91                                                                                                   A‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAATATGAC  >  2:776832/1‑91                                                                                                                                                                                                GTTATTAGGACATATAAATTCATCATTAAGTTCGTCATATTTCCAATTTTGAGTGTTGAAAATGTCACTTTTAAACTTTCTAGTTTTATCTTTAATAAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1912028‑1911930 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tttaataaa‑ACGCCACTTATTACGTATGGCATGTTTATTAAAGATAAAACTAGAAAGTTTAAAAGTGACATTTTCAACACTTAAAATTGGAAATATGAC  >  USA300TCH1516_ALE/2318846‑2318935

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ 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.