New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 580753	144 (0.710)	13 (0.080)	7/130	NT	9.6%	intergenic (+47/‑34)	USA300HOU_RS02805/sigH	hypothetical protein/RNA polymerase sigma‑H factor
	?	USA300TCH1516_ALE	= 580772	129 (0.780)					intergenic (+66/‑15)	USA300HOU_RS02805/sigH	hypothetical protein/RNA polymerase sigma‑H factor

TCTTCTGAAATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/580650‑580753 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aatattaaactaaccCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTTCG  <  USA300TCH1516_ALE/580772‑580683                                                                                                                                                                                                    TCTTCTGAAATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAA                                                                                                         <  1:1542114/91‑1   TTCTGAAATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATA                                                                                                       >  2:1908516/1‑91   TTCTGAAATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATA                                                                                                       >  2:638055/1‑91   TTCTGAAATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCCTGAAATTTTGAATGTAACAATA                                                                                                       >  2:3189486/1‑91   TTCTGAAATCCTTGCAGAATTAGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATA                                                                                                       <  2:3653411/91‑1    TCTGAAATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATAT                                                                                                      <  1:1256970/91‑1    TCTGAAATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATAT                                                                                                      >  1:2411220/1‑91    TCTGAAATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATAT                                                                                                      <  2:2110232/91‑1    TCTGAAATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATAT                                                                                                      <  1:2762372/91‑1     CTGAAATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATT                                                                                                     >  1:1333447/1‑91     CTGAAATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATT                                                                                                     >  1:943287/1‑91     CTGAAATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATT                                                                                                     >  1:407864/1‑91     CTGAAATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACACTTCCGTCATCTTGAAATTTTGAATGTAACAATATT                                                                                                     >  2:3866967/1‑91        AAATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAA                                                                                                  <  2:2912874/91‑1        AAATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAA                                                                                                  <  2:2630310/91‑1        AAATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAA                                                                                                  <  2:2629426/91‑1         AATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAAC                                                                                                 >  1:1108302/1‑91         AATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAAC                                                                                                 >  1:1723026/1‑91          ATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACT                                                                                                >  1:3282981/1‑91          ATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACT                                                                                                >  1:3282775/1‑91           TCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTA                                                                                               <  2:1233655/91‑1            CCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAA                                                                                              >  2:1231668/1‑91             CTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAAC                                                                                             >  1:909829/1‑91             CTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAAC                                                                                             >  1:909599/1‑91             CTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAAC                                                                                             <  1:90552/91‑1             CTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAAC                                                                                             <  2:764878/91‑1              TTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAACC                                                                                            <  1:3322175/91‑1              TTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAACC                                                                                            >  1:382177/1‑91              TTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAACC                                                                                            <  1:544430/91‑1                                   GAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAACCCCTTCTATCTAAAATTTAAGG                                                                       <  2:1524486/91‑1                                    AAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGT                                                                      <  2:369202/91‑1                                    AAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGT                                                                      <  2:369373/91‑1                                    AAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGT                                                                      <  1:771415/91‑1                                    AAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGT                                                                      <  1:771248/91‑1                                    AAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGT                                                                      <  1:771270/91‑1                                     AGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTT                                                                     <  1:1777728/91‑1                                     AGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTT                                                                     <  2:1219409/91‑1                                       AGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAG                                                                   <  1:2180858/91‑1                                        GGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGT                                                                  <  1:3877923/91‑1                                           CATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTA                                                               <  1:2851446/91‑1                                           CATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTA                                                               <  1:2852009/91‑1                                            ATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAACCCCTTCTATCTAAAATTTTAGGTTAGTTTAA                                                              <  1:3036677/91‑1                                                                                          AATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTA                <  2:3038075/91‑1                                                                                          AATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTA                <  2:18473/91‑1                                                                                           ATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTAT               <  1:931226/91‑1                                                                                           ATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTAT               <  2:1140210/91‑1                                                                                            TATTAAACTAACCCCTTCTATCTAAGATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATG              <  2:2893248/91‑1                                                                                            TATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATG              <  2:3417624/91‑1                                                                                             ATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGA             >  2:3264263/1‑91                                                                                              TTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGAT            >  1:975215/1‑91                                                                                              TTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGAT            >  1:2939632/1‑91                                                                                              TTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGAT            >  1:2940779/1‑91                                                                                              TTAAACTAACCCCTTCTATCGAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGAT            <  2:2387575/91‑1                                                                                               TAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATG           >  2:487309/1‑91                                                                                               TAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATG           <  1:3342630/91‑1                                                                                                 AACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAGTGTCATTTCTTATGATGTC         >  1:166389/1‑91                                                                                                 AACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTC         >  1:1051412/1‑91                                                                                                 AACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTC         >  1:166418/1‑91                                                                                                 AACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTC         >  1:1607484/1‑91                                                                                                 AACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTC         >  2:3355217/1‑91                                                                                                 AACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTC         >  1:3439803/1‑91                                                                                                  ACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCC        >  1:354169/1‑91                                                                                                   CTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTAGATTCAAAAGTTCCAGATGACGGAAATGTCATTTCTTATGATGTCCT       <  1:3149935/91‑1                                                                                                    TAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTC      >  2:3808812/1‑91                                                                                                    TAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTC      >  2:2562847/1‑91                                                                                                     AACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCT     >  1:2997777/1‑91                                                                                                     AACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCT     <  1:1139274/91‑1                                                                                                      ACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTT    >  2:2786316/1‑91                                                                                                      ACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTT    <  1:397743/91‑1                                                                                                      ACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTT    >  1:810698/1‑91                                                                                                      ACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTT    <  2:2675987/91‑1                                                                                                       CCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAACTGTCATTTCTTATGATGTCCTCTTC   >  2:2388276/1‑91                                                                                                       CCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTTC   <  1:28190/91‑1                                                                                                       CCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTTC   <  1:28234/91‑1                                                                                                       CCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTTC   >  2:121356/1‑91                                                                                                       CCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTTC   >  2:300014/1‑91                                                                                                       CCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTTC   <  2:296391/91‑1                                                                                                       CCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTTC   >  1:2475348/1‑91                                                                                                       CCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAAGTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTTC   >  2:3483008/1‑91                                                                                                       CCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAACTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTTC   >  2:3482932/1‑91                                                                                                       CCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAAATTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTTC   >  2:3482754/1‑91                                                                                                       CCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAAATTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTTC   >  2:3482931/1‑91                                                                                                        CCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTTCG  <  2:1198660/91‑1                                                                                                        CCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTTCG  <  2:1276113/91‑1                                                                                                        CCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTTCG  >  1:1885439/1‑91                                                                                                        CCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTTCG  <  2:252099/91‑1                                                                                                                                                                                                    TCTTCTGAAATCCTTGCAGAATTTGAAAAAATACGAAGAGGACATCATAAGAAATGACATTTCCGTCATCTTGAAATTTTGAATGTAACAATATTAAACTAACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/580650‑580753 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aatattaaactaaccCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTGTTACATTCAAAATTTCAAGATGACGGAAATGTCATTTCTTATGATGTCCTCTTCG  <  USA300TCH1516_ALE/580772‑580683

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.