New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 161203	321 (0.900)	18 (0.050)	11/150	NT	5.3%	coding (730/816 nt)	phnE_1	Phosphate‑import permease protein PhnE
	?	USA300TCH1516_ALE	= 161213	338 (1.010)					coding (720/816 nt)	phnE_1	Phosphate‑import permease protein PhnE

ATTTAATGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/161109‑161203 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑acacgTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTAT  <  USA300TCH1516_ALE/161213‑161124                                                                                                                                                                                           ATTTAATGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTA                                                                                                >  1:5348665/1‑91 ATTTAATGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTA                                                                                                <  2:1162439/91‑1 ATTTAATGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTA                                                                                                >  1:5349207/1‑91 ATTTAATGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTA                                                                                                <  1:4562890/91‑1 ATTTAATGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTA                                                                                                >  2:510809/1‑91 ATTTAATGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTA                                                                                                <  1:1617688/91‑1 ATTTAATGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTA                                                                                                <  2:897160/91‑1  TTTAATGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTAC                                                                                               >  2:261986/1‑91  TTTAATGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTAC                                                                                               <  1:6597868/91‑1   TTAATGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACA                                                                                              >  1:4507895/1‑91   TTAATGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACA                                                                                              <  2:4865201/91‑1    TAATGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACAC                                                                                             <  1:1442992/91‑1     AATGTTAAACACTACGTTTTCGGATTGAACCGGAAATTAAATCGACAATCGCGACCATTAGTACTAAACCGATTAATATGATACCTACACG                                                                                            >  2:6965431/1‑91     AATGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACG                                                                                            >  1:732188/1‑91     AATGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACG                                                                                            >  2:2372221/1‑91     AATGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACG                                                                                            <  2:2926061/91‑1     AATGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACG                                                                                            >  1:730622/1‑91       TGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACGTT                                                                                          <  2:1389699/91‑1           AAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACGTTCTTG                                                                                      >  1:6889644/1‑91            AACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACGTTCTTGG                                                                                     <  2:1165048/91‑1            AACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACGTTCTTGG                                                                                     <  1:3992834/91‑1            AACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACGTTCTTGG                                                                                     <  1:3991433/91‑1             ACAATACGTTTTCGGATTGAACCGGATATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACGTTCTTGGG                                                                                    <  2:6889644/91‑1             ACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACGTTCTTGGG                                                                                    <  2:432496/91‑1             ACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACGTTCTTGGG                                                                                    <  1:922909/91‑1             ACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACGTTCTTGGG                                                                                    <  2:3608238/91‑1             ACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACGTTCTTGGG                                                                                    <  1:2506747/91‑1             ACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACGTTCTTGGG                                                                                    <  2:4610439/91‑1              CAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACGTTCTTGGGA                                                                                   <  1:3129450/91‑1                                                  CAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACGGTCCCAAGAACGTGTAGGTATTATATTAATCGGTCTAGTACTAAT                                               >  2:886804/1‑91                                                    ATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACGGTCCCAAGAACGTGTAGGTATTATATTAATCGGTTTAGTACTAATGG                                             >  2:1276602/1‑91                                                                 GTACTAAACCGATTAATATAATACCTACACGGTCCCAAGAACGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGA                                >  1:1283856/1‑91                                                                      AAACCGATTAATATAATACCTACACGGTCCCAAGAACGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAA                           >  2:5701520/1‑91                                                                           GATTAATATAATACCTACACGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCC                      <  2:951997/91‑1                                                                             TTAATATAATACCTACACGGTCCCAAGAACGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCACTTGTCGATTTAATTTCCGG                    >  2:2106141/1‑91                                                                               AATATAATACCTACACGGTCCCAAGAACGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTT                  >  2:4028238/1‑91                                                                                           ACACGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGCAAAC      >  2:5597902/1‑91                                                                                           ACACGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAAC      <  2:1693546/91‑1                                                                                           ACACGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAAC      >  1:1532143/1‑91                                                                                           ACACGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAAC      <  1:5990307/91‑1                                                                                            CACGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACG     <  1:731302/91‑1                                                                                             ACGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGT    <  1:6357574/91‑1                                                                                             ACGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGT    <  1:6362292/91‑1                                                                                             ACGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGT    <  2:4244287/91‑1                                                                                             ACGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGT    <  1:6121128/91‑1                                                                                             ACGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGT    >  2:6264844/1‑91                                                                                             ACGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGT    >  2:6065468/1‑91                                                                                              CGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTA   >  2:2224922/1‑91                                                                                              CGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTA   >  2:922703/1‑91                                                                                              CGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTA   >  2:224240/1‑91                                                                                              CGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTA   >  1:2032400/1‑91                                                                                              CGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTA   <  1:396424/91‑1                                                                                              CGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTA   >  2:6662695/1‑91                                                                                              CGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTA   >  2:6060923/1‑91                                                                                              CGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTA   >  2:5832776/1‑91                                                                                              CGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTA   >  1:4254795/1‑91                                                                                              CGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTA   <  1:534495/91‑1                                                                                              CGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTA   >  1:6650001/1‑91                                                                                              CGTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTA   >  2:4180396/1‑91                                                                                               GTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTAT  >  1:686103/1‑91                                                                                               GTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTAT  >  1:6788014/1‑91                                                                                               GTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTAT  <  1:3722886/91‑1                                                                                               GTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTAT  >  2:2896472/1‑91                                                                                               GTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTAT  <  2:3673802/91‑1                                                                                               GTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTGCCGGTTCAATCCGAAAACGTAT  <  2:5329640/91‑1                                                                                                                                                                                           ATTTAATGTTAAACAATACGTTTTCGGATTGAACCGGAAATTAAATCGACAATTGCGACCATTAGTACTAAACCGATTAATATAATACCTACACG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/161109‑161203 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑acacgTTCTTGGGACCGTGTAGGTATTATATTAATCGGTTTAGTACTAATGGTCGCAATTGTCGATTTAATTTCCGGTTCAATCCGAAAACGTAT  <  USA300TCH1516_ALE/161213‑161124

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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.