New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 441303	155 (0.760)	24 (0.130)	12/142	NT	13.8%	intergenic (+20/+93)	guaA/USA300HOU_RS02075	GMP synthase [glutamine‑hydrolyzing]/hypothetical protein
	?	USA300TCH1516_ALE	= 441313	163 (0.900)					intergenic (+30/+83)	guaA/USA300HOU_RS02075	GMP synthase [glutamine‑hydrolyzing]/hypothetical protein

CGTAAACGAAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/441205‑441303 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaaccaccCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCGGTTGAC  <  USA300TCH1516_ALE/441313‑441224                                                                                                                                                                                               CGTAAACGAAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATA                                                                                                    <  2:1803616/91‑1  GTAAACGAAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAA                                                                                                   >  1:1452759/1‑91   TAAACGAAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAA                                                                                                  <  2:576390/91‑1   TAAACGAAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAA                                                                                                  <  2:2889830/91‑1   TAAACGAAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAA                                                                                                  <  2:1236788/91‑1    AAACGAAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAA                                                                                                 <  1:2691996/91‑1    AAACGAAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAA                                                                                                 >  1:434719/1‑91    AAACGAAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAA                                                                                                 >  1:1641999/1‑91    AAACGAAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAA                                                                                                 >  2:190291/1‑91    AAACGAAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAA                                                                                                 >  1:2018542/1‑91     AACGAAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAAC                                                                                                <  1:1793596/91‑1      ACGAAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACC                                                                                               >  1:3231870/1‑91       CGAAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCA                                                                                              <  2:3271311/91‑1       CGAAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCA                                                                                              >  2:1023235/1‑91       CGAAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCA                                                                                              >  1:527396/1‑91        GAAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCAC                                                                                             <  2:2726230/91‑1         AAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACC                                                                                            >  1:3252784/1‑91         AAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACC                                                                                            >  2:89915/1‑91         AAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACC                                                                                            >  1:3090275/1‑91              GATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGC                                                                                       <  2:2352238/91‑1               ATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCA                                                                                      <  1:3587798/91‑1                TCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAA                                                                                     <  2:2367648/91‑1                TCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAA                                                                                     <  1:22200/91‑1                 CACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAAA                                                                                    <  2:2259442/91‑1                 CACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAAA                                                                                    <  2:2259539/91‑1                 CACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAAA                                                                                    <  2:2015535/91‑1                 CACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAAA                                                                                    <  2:3495105/91‑1                 CACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAAA                                                                                    <  2:416241/91‑1                  ACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAAAC                                                                                   <  1:1085949/91‑1                  ACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAAAC                                                                                   <  1:392533/91‑1                   CGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAAACA                                                                                  <  2:2621064/91‑1                    GTCAACCGCGTAGTCTATGACATTACATCAAAACCGCCAAGCACAATTGAGTGGGAATAATTATATATGATAAAACCACCCGTGCAAACAG                                                                                 <  2:2323057/91‑1                    GTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAAACAG                                                                                 <  1:2292870/91‑1                    GTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAAACAG                                                                                 <  2:3081846/91‑1                    GTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAAACAG                                                                                 <  2:1727483/91‑1                       AACCGCGTAGTCTATGACATTACATCAAGACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAAACAGGTG                                                                              <  2:2385876/91‑1                       AACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAAACAGGTG                                                                              <  2:2385775/91‑1                       AACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAAACAGGTG                                                                              <  2:2385897/91‑1                       AACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAAACAGGTG                                                                              <  2:1326166/91‑1                        ACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAAACAGGTGG                                                                             <  1:710491/91‑1                             GTAGTCTATGATATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACCCGTGCAAACAGGTGGTTTTA                                                                        <  1:3626438/91‑1                                                                              AATTATATATAATAAAACCACCTGTTTGCACGGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAAT                       >  1:1914718/1‑91                                                                                  ATATATAATAAAACCACCTGTTTGCACGGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCA                   >  1:1756525/1‑91                                                                                   TATATAATAAAACCACCTGTTTGCACGGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCAT                  >  2:608517/1‑91                                                                                           AAAACCACCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCGCTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACG          >  1:3954701/1‑91                                                                                            AAACCACCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGC         >  1:2020012/1‑91                                                                                            AAACCACCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGC         >  1:1753587/1‑91                                                                                             AACCACCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCG        <  1:1101328/91‑1                                                                                             AACCACCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCG        <  1:1012552/91‑1                                                                                             AACCACCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCG        >  1:657890/1‑91                                                                                              ACCACCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCGG       >  2:818479/1‑91                                                                                              ACCACCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCGG       <  1:707044/91‑1                                                                                              ACCACCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCGG       >  2:1645395/1‑91                                                                                              ACCACCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTCTTGATGTAATGTCATAGACTACGCGG       >  1:1243609/1‑91                                                                                              ACCACCCGTGCAAACAGGTGGTTTTATTATATATAATTATCCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCGG       >  2:3621749/1‑91                                                                                               CCACCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCGGT      >  2:2085135/1‑91                                                                                               CCACCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCGGT      <  2:1763688/91‑1                                                                                               CCACCCGTGCAAAAAGGTGGTTTTTTTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTACGGTCATAGACTCCGCGGT      >  2:895983/1‑91                                                                                                CACCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCATTTGTGCTTGGTGGTTTTGATGTAATGTCACAGACTACGCGGTT     >  1:3962914/1‑91                                                                                                CACCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCGGTT     <  1:2349967/91‑1                                                                                                CACCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCGGTT     >  2:2626582/1‑91                                                                                                 ACCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGGGGTTTTGATGTAATGTCATAGACTACGCGGTTG    >  1:2265566/1‑91                                                                                                  CCCGTGCAAACAGGTGGTTTTATTATATATAATTATTTCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCGGTTGA   >  1:2827597/1‑91                                                                                                  CCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCGGTTGA   >  1:613629/1‑91                                                                                                  CCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCGGTTGA   <  1:3728061/91‑1                                                                                                  CCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCGGTTGA   >  2:2246401/1‑91                                                                                                  CCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCGGTTGA   >  2:2569771/1‑91                                                                                                  CCCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCGGTTGA   >  2:2566278/1‑91                                                                                                   CCGTGCAAACAGGTGGTTTTATTATATATAATTATTGCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCGGTTGAC  <  2:3114986/91‑1                                                                                                   CCGTGCAAACAGGTGGTTTTATTATATATAATTATGCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCGGTTGAC  <  2:564682/91‑1                                                                                                                                                                                               CGTAAACGAAGTAGATCACGTCAACCGCGTAGTCTATGACATTACATCAAAACCACCAAGCACAATTGAGTGGGAATAATTATATATAATAAAACCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/441205‑441303 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaaccaccCGTGCAAACAGGTGGTTTTATTATATATAATTATTCCCACTCAATTGTGCTTGGTGGTTTTGATGTAATGTCATAGACTACGCGGTTGAC  <  USA300TCH1516_ALE/441313‑441224

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.