New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1616458	169 (0.830)	10 (0.050)	9/144	NT	5.6%	intergenic (‑43/‑39)	nudF/yhdN_2	ADP‑ribose pyrophosphatase/General stress protein 69
	?	USA300TCH1516_ALE	= 1616473	184 (1.000)					intergenic (‑58/‑24)	nudF/yhdN_2	ADP‑ribose pyrophosphatase/General stress protein 69

CAATTTTGCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1616361‑1616458 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gatacactTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGATCGAAC  <  USA300TCH1516_ALE/1616473‑1616384                                                                                                                                                                                              CAATTTTGCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCAGATTATATATTG                                                                                                   >  1:3581918/1‑91 CAATTTTGCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCACATTATATATTG                                                                                                   >  1:3582033/1‑91  AATTTTGCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGA                                                                                                  >  2:1750804/1‑91   ATTTTGCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGAT                                                                                                 <  2:2763043/91‑1   ATTTTGCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGAT                                                                                                 >  1:3358777/1‑91    TTTTGCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATA                                                                                                >  2:2657352/1‑91     TTTGCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAGATTCATATTATATATTGATAC                                                                                               <  2:1606263/91‑1     TTTGCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATAC                                                                                               <  2:267897/91‑1     TTTGCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATAC                                                                                               <  2:267870/91‑1     TTTGCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATAC                                                                                               <  2:1779804/91‑1      TTGCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACA                                                                                              >  1:1275030/1‑91      TTGCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACA                                                                                              <  2:658856/91‑1       TGCCCTTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATGCAC                                                                                             >  1:3121958/1‑91       TGCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAATTCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACAC                                                                                             >  2:1379835/1‑91       TGCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACAC                                                                                             >  1:849230/1‑91        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTTTTTTTTTTTCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATATACT                                                                                            >  2:1328658/1‑91        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTTTTTTTTTTCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT                                                                                            >  2:103492/1‑91        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTTATTTTATTCTTTTATAATCACGTTCCTTTAATTTTATATTATATATTGATACACT                                                                                            >  2:429704/1‑91        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTATATCCTTTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT                                                                                            >  2:95131/1‑91        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCTTTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT                                                                                            >  2:2829594/1‑91        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT                                                                                            <  2:303292/91‑1        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT                                                                                            >  1:2347184/1‑91        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT                                                                                            >  1:1941754/1‑91        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT                                                                                            <  2:1953722/91‑1        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT                                                                                            <  2:2029261/91‑1        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT                                                                                            <  1:3000105/91‑1        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT                                                                                            >  2:3505721/1‑91        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT                                                                                            <  2:3818397/91‑1        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT                                                                                            <  2:3818412/91‑1        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT                                                                                            >  2:429451/1‑91        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT                                                                                            >  2:519143/1‑91        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT                                                                                            >  2:99249/1‑91        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT                                                                                            <  1:3000133/91‑1        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT                                                                                            >  2:1328431/1‑91        GCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT                                                                                            >  1:330089/1‑91                      CTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACTTTAGCTAACAAGCA                                                                              <  2:2467933/91‑1                        GTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACTTTAGCTAACAAGCATA                                                                            <  2:2138057/91‑1                         TTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACTTTAGCTAACAAGCATAG                                                                           <  2:2384479/91‑1                            GATCAATTGCTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACTTTAGCTAACAAGCATAGTGT                                                                        <  1:3547910/91‑1                                AATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACTTTAGCTAACAAGCATAGTGTATCA                                                                    <  1:1694990/91‑1                                 ATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATCGATACACTTTAGCTAACAAGCATAGTGTATCAA                                                                   <  1:278132/91‑1                                  TTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACTTTAGCTAACAAGCATAGTGTATCAAT                                                                  <  2:3339098/91‑1                                          TCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACTTTAGCTAACAAGCATAGTGTATCAATATATAATA                                                          <  1:1260715/91‑1                                            ATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATCGATACACTTTAGCTAACAAGCATAGTGTATCAATATATAATATG                                                        <  2:411433/91‑1                                            ATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATCGATACACTTTAGCTAACAAGCATAGTGTATCAATATATAATATG                                                        <  2:411466/91‑1                                                                                           GATACACTTTAGCTAACAAGCATAGTGTATCAATATATAATCTGAATTTAAAGGAACGTGATTATAATCGATTTAAATGAAAAAACAATTG         >  2:3001685/1‑91                                                                                           GATACACTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTG         <  1:676763/91‑1                                                                                           GATACACTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTG         <  1:1941126/91‑1                                                                                            ATACACTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGA        >  2:282778/1‑91                                                                                            ATACACTTGAGATAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGAAATAAAAGAAAAAACAATTGA        <  2:1556778/91‑1                                                                                             TACACTTTAGCTAACAAGCATAGTGTATCCATATATAATATGAATTTAAAGGCACGTGATTATAATGGATTTAAATGAAAAAACAATTGAT       >  2:1068328/1‑91                                                                                             TACACTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGAT       >  1:1759047/1‑91                                                                                             TACACTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGAT       >  2:1068689/1‑91                                                                                             TACACTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGAT       >  2:396547/1‑91                                                                                             TACACTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGAT       <  1:2476077/91‑1                                                                                                ACTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGATCGA    >  1:2516923/1‑91                                                                                                ACTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGATCGA    >  2:1164937/1‑91                                                                                                ACTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGATCGA    >  2:2021784/1‑91                                                                                                ACTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGATCGA    <  1:1652734/91‑1                                                                                                ACTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGATCGA    >  2:2022111/1‑91                                                                                                ACTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGATCGA    >  1:464654/1‑91                                                                                                ACTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGATCGA    >  1:464905/1‑91                                                                                                 CTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGATCGAA   <  1:3813014/91‑1                                                                                                 CTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGATCGAA   >  2:3479896/1‑91                                                                                                 CTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGATCGAA   >  1:924062/1‑91                                                                                                 CTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGATCGAA   <  1:2773372/91‑1                                                                                                 CTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGATCGAA   <  2:2651265/91‑1                                                                                                 CTTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGATCGAA   <  2:819201/91‑1                                                                                                  TTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGATCGAAC  >  2:1837478/1‑91                                                                                                  TTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGATCGAAC  <  1:1410178/91‑1                                                                                                                                                                                              CAATTTTGCCATTATAAATAACTGTTCGATCAATTGTTTTTTCATTTAAATCCATTATAATCACGTTCCTTTAAATTCATATTATATATTGATACACT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1616361‑1616458 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gatacactTTAGCTAACAAGCATAGTGTATCAATATATAATATGAATTTAAAGGAACGTGATTATAATGGATTTAAATGAAAAAACAATTGATCGAAC  <  USA300TCH1516_ALE/1616473‑1616384

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.