New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1255833 =	96 (0.980)	8 (0.090)	4/138	NT	9.5%	intergenic (+49/+195)	rplS/USA300HOU_RS06250	50S ribosomal protein L19/hypothetical protein
	?	USA300TCH1516_ALE	1255876 =	70 (0.830)					intergenic (+92/+152)	rplS/USA300HOU_RS06250	50S ribosomal protein L19/hypothetical protein

TGAATAGAGAAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCTAGATGGCTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1255933‑1255833 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tagatggctttTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACA  >  USA300TCH1516_ALE/1255876‑1255965                                                                                                                                                                                                 TGAATAGAGAAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCT                                                                                                      >  1:825827/1‑91  GAATAGAGAAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCTA                                                                                                     <  1:1644136/91‑1    ATAGAGAAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCTAGA                                                                                                   >  1:4069389/1‑91    ATAGAGAAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACATAGA                                                                                                   >  1:3454957/1‑91     TAGAGAAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCTAGAT                                                                                                  <  1:3720698/91‑1     TAGAGAAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCTAGAT                                                                                                  <  1:546350/91‑1     TAGAGAAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCTAGAT                                                                                                  <  1:3038645/91‑1     TAGAGAAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCTAGAT                                                                                                  <  1:546922/91‑1       GAGAAGGAATAAACAATTACATTATCAACTTTACATTAACTAACCAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCTAGATGG                                                                                                <  1:630820/91‑1       GAGAAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCTAGATGG                                                                                                <  1:936645/91‑1       GAGAAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCTAGATGG                                                                                                <  1:630198/91‑1       GAGAAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGC‑AAAAAAGCCATCTATATCACTCCATAAAAGTGACCTAGATGGC                                                                                               <  1:3372960/91‑1        AGAAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCTAGATGGC                                                                                               <  1:1746036/91‑1        AGAAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCTAGATGGC                                                                                               <  1:322067/91‑1        AGAAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCTAGATGGC                                                                                               <  1:322066/91‑1         GAAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCTAGATGGCT                                                                                              <  1:1373312/91‑1         GAAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCTAGATGGCT                                                                                              >  1:407667/1‑91          AAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCTAGATGGCTT                                                                                             <  1:1368181/91‑1           AGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCTAGATGGCTTT                                                                                            >  1:3381542/1‑91                                                             AGCCATCTATATCACTCCATAAAAGTGACCTAGATGGCTTTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTC                                          >  1:988262/1‑91                                                             AGCCATCTATATCACTCCATAAAAGTGACCTAGATGGCTTTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTC                                          >  1:2030097/1‑91                                                              GCCATCTATATCACTCCATAAAAGTGACCTAGATGGCTTTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCT                                         >  1:1503440/1‑91                                                              GCCATCTATATCACTCCATAAAAGTGACCTAGATGGCTTTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCT                                         >  1:1503566/1‑91                                                                CATCTATATCACTCCATAAAAGTGACCTAGATGGCTTTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCT                                       >  1:1323845/1‑91                                                                CATCTATATCACTCCATAAAAGTGACCTAGATGGCTTTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCT                                       >  1:1323125/1‑91                                                                 ATCTATATCACTCCATAAAAGTGACCTAGATGGCTTTGTTTGCTGTCTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTA                                      >  1:3302290/1‑91                                                                 ATCTATATCACTCCATAAAAGTGACCTAGATGGCTTTATTTGCTGTCTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTA                                      >  1:3302343/1‑91                                                                                            AGATGGCTTTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTT           >  1:2432365/1‑91                                                                                             GATGGCTTTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTA          <  1:2646231/91‑1                                                                                               TGGCTTTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATA        >  1:4031455/1‑91                                                                                               TGGCTTTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATA        <  1:1904724/91‑1                                                                                               TGGCTTTTTATGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATA        >  1:2088284/1‑91                                                                                                GGCTTTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATAT       <  1:11848/91‑1                                                                                                GGCTTTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATAT       <  1:11596/91‑1                                                                                                 GCTTTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATA      >  1:3093364/1‑91                                                                                                 GCTTTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATA      >  1:3092653/1‑91                                                                                                   TTTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAA    <  1:3939873/91‑1                                                                                                   TTTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAA    <  1:3940066/91‑1                                                                                                   TTTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAA    >  1:3993890/1‑91                                                                                                    TTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAAC   <  1:3899942/91‑1                                                                                                    TTTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAAC   <  1:1045187/91‑1                                                                                                     TTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACA  <  1:532949/91‑1                                                                                                                                                                                                 TGAATAGAGAAGGAATAAACAATTACATTATCAACTTTACATTAACTAAACAGCAAAAAAAGCCATCTATATCACTCCATAAAAGTGACCTAGATGGCTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1255933‑1255833 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tagatggctttTTTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACA  >  USA300TCH1516_ALE/1255876‑1255965

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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.