New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000731	= 22941	475 (0.850)	23 (0.050)	13/146	NT	5.0%	coding (1398/1467 nt)	USA300HOU_pUSA300HOUMR0028	macrolide transporter
	?	CP000731	= 22955	440 (0.870)					coding (1412/1467 nt)	USA300HOU_pUSA300HOUMR0028	macrolide transporter

TGAACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP000731/22845‑22941 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tgatacaTGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTTTTAATA  <  CP000731/22955‑22866                                                                                                                                                                                             TGAACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACAT                                                                                                  >  1:1138678/1‑91 TGAACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACAT                                                                                                  >  1:1138726/1‑91 TGAACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACAT                                                                                                  >  1:811331/1‑91  GAACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATG                                                                                                 <  2:3310388/91‑1  GAACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATG                                                                                                 <  2:519080/91‑1  GAACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATG                                                                                                 >  2:2468536/1‑91  GAACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATG                                                                                                 >  1:2890149/1‑91  GAACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATG                                                                                                 <  2:3310098/91‑1  GAACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATG                                                                                                 <  1:140664/91‑1   AACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGA                                                                                                >  1:1678075/1‑91   AACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGA                                                                                                >  1:944512/1‑91   AACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGA                                                                                                <  2:3537037/91‑1   AACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGA                                                                                                >  2:2128906/1‑91   AACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGA                                                                                                >  2:2129797/1‑91    ACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGAT                                                                                               <  1:85158/91‑1    ACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGAT                                                                                               <  2:2254025/91‑1    ACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGAT                                                                                               <  2:3522117/91‑1     CCAACTAATTTTTTAGATATTAATACATTAGAAGCATTAGAAATGTTTATGAATAACTATCCTGGATTCTTTTTGTTTACATCTCATGATA                                                                                              >  2:1046907/1‑91     CCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATA                                                                                              <  1:1497368/91‑1     CCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATA                                                                                              <  1:2106318/91‑1     CCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATA                                                                                              <  2:3169647/91‑1     CCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTCATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATA                                                                                              <  2:2995824/91‑1      CAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATAC                                                                                             <  1:3685373/91‑1      CAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATAC                                                                                             <  2:2726060/91‑1      CAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATAC                                                                                             <  1:737546/91‑1      CAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATAC                                                                                             >  2:482239/1‑91      CAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATAC                                                                                             <  2:25371/91‑1      CAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATAC                                                                                             <  2:1109794/91‑1      CAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATAC                                                                                             <  2:996564/91‑1      CAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATAC                                                                                             <  1:1222950/91‑1      CAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATAC                                                                                             <  2:99394/91‑1      CAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATAC                                                                                             <  2:651553/91‑1      CAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATAC                                                                                             <  1:1779761/91‑1       AACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACA                                                                                            <  1:105070/91‑1       AACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTATATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACA                                                                                            <  1:3085766/91‑1        ACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACA                                                                                            >  2:1396104/1‑90        ACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACA                                                                                            <  1:1396104/90‑1        ACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACA                                                                                            <  1:1396512/90‑1        ACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACA                                                                                            >  2:1396512/1‑90                  TAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAA                                                                                 <  2:2562991/91‑1                   AGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAAC                                                                                <  2:2125797/91‑1                     ATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCT                                                                              <  1:1463799/91‑1                     ATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCT                                                                              <  2:2924174/91‑1                       ATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCTTG                                                                            <  1:909629/91‑1                       ATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCTTG                                                                            <  2:64414/91‑1                       ATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCTTG                                                                            <  1:501847/91‑1                        TTAAAACATTAGAAGCATTAGAAATGTTTATGAATAGATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCTTGT                                                                           <  2:1623454/91‑1                         TAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCTTGTA                                                                          <  2:1491275/91‑1                         TAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCTTGTA                                                                          <  1:200146/91‑1                         TAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCTTGTA                                                                          <  1:1978516/91‑1                         TAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCTTGTA                                                                          <  2:76625/91‑1                         TAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCTTGTA                                                                          <  1:461338/91‑1                         TAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCTTGTA                                                                          <  2:3818985/91‑1                         TAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCTTGTA                                                                          <  1:1878189/91‑1                          AAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCTTGTAT                                                                         <  2:787436/91‑1                              CATTAGAAGCATTAGAAATGTTTATGAATAAGTATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCTTGTATCATG                                                                     <  2:2452171/91‑1                              CATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCTTGTATCATG                                                                     <  1:3734312/91‑1                               ATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCTTGTATCATGT                                                                    <  1:3200793/91‑1                                TTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCTTGTATCATGTG                                                                   <  2:2224722/91‑1                                  AGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCTTGTATCATGTGAT                                                                 <  1:1041611/91‑1                                   GAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGGTTAACAAACCTTGTATCATGTGATG                                                                <  2:2532968/91‑1                                    AAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACATGTTTAACAAACCTTGTATCATGTGATGT                                                               <  1:2332746/91‑1                                                                                           TGATACATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTT        >  2:2498947/1‑91                                                                                           TGATACATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTT        >  2:421083/1‑91                                                                                           TGATACATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTT        <  1:3757916/91‑1                                                                                           TGATACATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTT        <  1:2214046/91‑1                                                                                           TGATACATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTT        <  2:3402237/91‑1                                                                                            GATACATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTTT       >  2:2833508/1‑91                                                                                             ATACATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTTTT      >  1:1048785/1‑91                                                                                             ATACATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTTTT      <  1:1075499/91‑1                                                                                             ATACATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTA             >  2:2335616/1‑84                                                                                             ATACATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTA             <  1:2335616/84‑1                                                                                              TACATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTTTTA     <  2:1308245/91‑1                                                                                               ACATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTTTTAA    >  2:3574797/1‑91                                                                                               ACATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTTTTAA    <  1:1341857/91‑1                                                                                                CATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTTTTAAT   >  2:1890274/1‑91                                                                                                CATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTTTTAAT   >  2:603890/1‑91                                                                                                 ATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAACCATTTCTAATGCTTCTAATGTTTTAATA  <  1:2524934/91‑1                                                                                                 ATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTTTTAATA  >  2:3416497/1‑91                                                                                                 ATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTTTTAATA  <  2:1260026/91‑1                                                                                                 ATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTTTTAATA  <  1:908790/91‑1                                                                                                 ATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTTTTAATA  <  1:2963828/91‑1                                                                                                 ATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTTTTAATA  <  1:2963636/91‑1                                                                                                 ATGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTTTTAATA  <  1:1337664/91‑1                                                                                                                                                                                             TGAACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP000731/22845‑22941 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tgatacaTGTTTAACAAACCTTGTATCATGTGATGTAAACAAAATGATTCCAGGATATTTATTCATAAACATTTCTAATGCTTCTAATGTTTTAATA  <  CP000731/22955‑22866

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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.