New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1678311	179 (0.880)	18 (0.110)	9/132	NT	9.9%	intergenic (+57/+93)	glyQS/recO	Glycine‑‑tRNA ligase/DNA repair protein RecO
	?	USA300TCH1516_ALE	= 1678323	179 (1.070)					intergenic (+69/+81)	glyQS/recO	Glycine‑‑tRNA ligase/DNA repair protein RecO

CAATCTCAGAGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1678208‑1678311 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaagagatactggCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTTTTTTCAGT  <  USA300TCH1516_ALE/1678323‑1678234                                                                                                                                                                                                    CAATCTCAGAGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAA                                                                                                         <  2:711106/91‑1  AATCTCAGAGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAA                                                                                                        <  2:2563841/91‑1  AATCTCAGAGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAA                                                                                                        <  1:88253/91‑1     CTCAGAGTTAGAAGCTTTCGTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAG                                                                                                     <  2:3237156/91‑1      TCAGAGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGA                                                                                                    <  2:367572/91‑1      TCAGAGTTAGAAGCTTTCTAAACTGAAAAGACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGA                                                                                                    >  2:3450989/1‑91       CAGAGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAG                                                                                                   >  1:2639071/1‑91       CAGAGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAG                                                                                                   >  1:2638975/1‑91       CAGAGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAG                                                                                                   <  1:195053/91‑1        AGAGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTCTAAAAAGAGA                                                                                                  >  1:1475695/1‑91        AGAGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGA                                                                                                  >  2:3352822/1‑91        AGAGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGA                                                                                                  >  1:2421096/1‑91        AGAGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTCCTGGCTATATGATTTATAAAAAGAGA                                                                                                  >  2:3424547/1‑91        AGAGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTACTGGCTATATCATTTATAAAAAGAGA                                                                                                  >  2:3425190/1‑91        AGAGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGAGGTGGCTATATAATTTATAAAAAGAGA                                                                                                  >  2:1927175/1‑91         GAGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGAT                                                                                                 >  2:1738808/1‑91         GAGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGAT                                                                                                 >  2:213770/1‑91         GAGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTACAAAAAGAGAT                                                                                                 >  2:3614986/1‑91          AGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATA                                                                                                >  1:1225079/1‑91          AGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATA                                                                                                >  1:3654155/1‑91          AGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATA                                                                                                >  1:3091219/1‑91           GTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATAC                                                                                               >  1:3716589/1‑91            TTAGAAGCTTTCTTAACTGAGAAAACAAAATTCTAATTAAAAAGACTTTCCGCCATATGTGGTGGCTATATAATTTATAAGAAGAGATACT                                                                                              <  2:42840/91‑1            TTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTAAATAAAAAATAAAAAGAGATACT                                                                                              <  2:42617/91‑1             TAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTG                                                                                             >  1:815667/1‑91             TAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTG                                                                                             >  2:2274282/1‑91             TAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTG                                                                                             >  2:896763/1‑91              AGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAATACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTGG                                                                                            <  2:3478781/91‑1                          AACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTGGCAATTTTACTAA                                                                                <  1:2983758/91‑1                           ACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCGTATGTGGTGGCTATATAATTTATAAAAAGAGATACTGGCAATTTTACTAAC                                                                               <  2:82771/91‑1                           ACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTGGCAATTTTACTAAC                                                                               <  2:2914111/91‑1                           ACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTGGCAATTTTACTAAC                                                                               <  2:82681/91‑1                           ACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTGGCAATTTTACTAAC                                                                               <  1:1003294/91‑1                           ACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTGGCAATTTTACTAAC                                                                               <  1:1003096/91‑1                            CTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTGGCAATTTTACTAACC                                                                              <  1:1529760/91‑1                            CTGAAAAAACAAAATTCTAATGAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTGGCAATTTTACTAACC                                                                              <  2:375604/91‑1                              GAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTGGCAATTTTACTAACCAG                                                                            <  1:422484/91‑1                              GAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTGGCAATTTTACTAACCAG                                                                            <  1:2636975/91‑1                              GAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTGGCAATTTTACTAACCAG                                                                            <  1:3870277/91‑1                                 AAAACAAAATTCTAGTTAAAAAGACTTTCCACCATATGTGGTGCCTATATAATGTATAAAAAGAGATACTGGCAATTTTACTAACCAGTAT                                                                         <  2:271920/91‑1                                   AACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTGGCAATTTTACTAACCAGTATCT                                                                       <  1:3761989/91‑1                                   AACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTGGCAATTTTACTAACCAGTATCT                                                                       <  2:2275824/91‑1                                     CAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTGGCAATTTTACTAACCAGTATCTCT                                                                     <  1:1130610/91‑1                                     CAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTGGCAATTTTACTAACCAGTATCTCT                                                                     <  1:1130650/91‑1                                               ATTAAAAAGACTTTCCACCATATGTGGTGTCTATATAATTTATAAAAAGAGATGCTGGCAATTTTACTAACCAGTATCTCTTTTTATAAAT                                                           <  2:1519111/91‑1                                                           TTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACC                                               <  1:3701270/91‑1                                                                                           AAAAGAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATT               <  2:1045724/91‑1                                                                                           AAAAGAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATT               >  2:1369666/1‑91                                                                                           AAAAGAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATT               <  2:2364755/91‑1                                                                                           AAAAGAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATT               <  2:2364728/91‑1                                                                                           AAAAGAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATT               >  1:3618662/1‑91                                                                                            AAAGAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATTTTTTCTTTAGCCACCACATATGGTTGAATGTCTTTTTAATTAGAATTT              >  2:1298964/1‑91                                                                                            AAAGAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTT              <  2:1224844/91‑1                                                                                            AAAGAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTT              <  1:2512662/91‑1                                                                                             AAGAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTT             <  1:3598875/91‑1                                                                                              AGAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTG            >  1:1427150/1‑91                                                                                              AGAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTG            <  1:2246757/91‑1                                                                                              AGAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTG            >  2:2975438/1‑91                                                                                              AGAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTG            >  2:1663449/1‑91                                                                                              AGAGATACTCGCAATTTTACTAACCAGTATCTCTTTTCATCAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTG            <  2:145675/91‑1                                                                                              AGAGAGACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTG            <  2:3640789/91‑1                                                                                               GAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGT           <  2:1591102/91‑1                                                                                               GAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGT           >  2:646541/1‑91                                                                                               GAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGT           >  2:646654/1‑91                                                                                               GAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGT           <  2:1591103/91‑1                                                                                               GAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGT           >  1:2026617/1‑91                                                                                               GAGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGT           >  1:2131926/1‑91                                                                                               GAGATACTGGCAATGTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGT           <  2:1591131/91‑1                                                                                                AGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTT          <  1:3621818/91‑1                                                                                                AGATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTT          <  1:3621735/91‑1                                                                                                AGATACTGGCAATTTTACTAACCAGTATCTCTTTTTAAAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTT          >  1:3331753/1‑91                                                                                                 GATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTTT         >  1:2463351/1‑91                                                                                                 GATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTTT         >  2:1495912/1‑91                                                                                                 GATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTTT         >  2:862410/1‑91                                                                                                 GATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTTT         <  1:1143099/91‑1                                                                                                  ATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTTTT        <  1:102018/91‑1                                                                                                  ATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTTTT        <  2:616278/91‑1                                                                                                  ATACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTTTT        >  2:1994150/1‑91                                                                                                    ACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTTTTTT      <  2:2625934/91‑1                                                                                                    ACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTTTTTT      >  2:352170/1‑91                                                                                                    ACTGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACAGATGGTGGAAAGTCTTTTTAATTAGAATTTTGTTTTTT      <  2:1573522/91‑1                                                                                                      TGGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTTTTTTCA    >  1:518355/1‑91                                                                                                       GGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTTTTTTCAG   >  1:1989768/1‑91                                                                                                       GGCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTTTTTTCAG   >  2:2006752/1‑91                                                                                                       GGCAATTTTACTAACCAGTATCGCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTGTAATTAGAATTTTGTTTGTTCAG   <  2:2556801/91‑1                                                                                                       GGCAATTTTACTAACCAGTAACTCTTTTTATAAATTATATAGCCACCACATATTGTGGAAAGTCTTTTTAATTAGAATTTTGTTTTTTCAG   <  1:1459175/91‑1                                                                                                        GCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTTTTTTCAGT  <  2:2674335/91‑1                                                                                                        GCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTTTTTTCAGT  <  2:2674141/91‑1                                                                                                                                                                                                    CAATCTCAGAGTTAGAAGCTTTCTTAACTGAAAAAACAAAATTCTAATTAAAAAGACTTTCCACCATATGTGGTGGCTATATAATTTATAAAAAGAGATACTGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1678208‑1678311 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaagagatactggCAATTTTACTAACCAGTATCTCTTTTTATAAATTATATAGCCACCACATATGGTGGAAAGTCTTTTTAATTAGAATTTTGTTTTTTCAGT  <  USA300TCH1516_ALE/1678323‑1678234

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.