New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	580739 =	104 (1.150)	4 (0.050)	3/250	9.4	4.1%	intergenic (+33/‑48)	USA300HOU_RS02805/sigH	hypothetical protein/RNA polymerase sigma‑H factor
	?	USA300TCH1516_ALE	580788 =	95 (1.170)					coding (2/570 nt)	sigH	RNA polymerase sigma‑H factor
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CGAATAATTAATGGTTGTAGATCCATTACTAACTTTTCGAAGTCTTTATCATTTATTGCATTGTTACGTTTGATTGTACTGTCTTGAGTTGTCAAATCGTATTTCAAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/580893‑580739 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ggttagtttaatattTGAAATACGATTTGACAACTCAAGACAGTACAATCAAACGTAACAATGCAATAAATGATAAAGACTTCGAAAAGTTAGTAATGGATCTACAACCATTAATTATTCGACGCATCAAAACATTTGGATTTAATCATTATGA  >  USA300TCH1516_ALE/580788‑580926                                                                                                                                                                                                                                                                                                        CGAATAATTAATGGTTGTAGATCCATTACTAACTTTTCGAAGTCTTTATCATTTATTGCATTGTTACGTTTGATTGTACTGTCTTGAGTTGTCAAATCGTATTTCAAATATTAAACTAACCCCTTCTATCTAAAATATAAG                                                                                                                                                           >  1:666959/1‑141  GAATAATTAATGGTTGTAGATCCATTACTAACTTTTCGAAGTCTTTATCATTTATTGCATTGTTACGTTTGATTGTACTGTCTTGAGTTGTCAAATCGTATTTCAAATATTAAACTAACCCCTTCTATCTAAAATTTAAGt                                                                                                                                                          >  2:761904/1‑140        TTAATGGTTTTAGATTCATTACTGACGTTTCGAAGTCTTTATCATTTATTGCATTGTTACGTTTGATTATACTGTCTTGAGTTGTCAAAGCGTATTTCAAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTT                                                                                                                                                    <  2:958165/141‑1        TTAATGGTTGTAGATCCATTACTAACTTTTCGAAGTCTTTATCATTTATTGCATTGTTACGTTTGATTGTACTGTCTTGAGTTGTCAAATCGTATTTCAAATGTTAAACTAACCCCTTCTACCTCAAATTTAAGGTTAGTT                                                                                                                                                    <  1:555517/141‑1        TTAATGGTTGTAGATCCATTACTAACTTTTCGAAGTCTTTATCATTTATTGCATTGTTACGTTTGATTGTACTGTCTTGAGTTGTCAAATCGTATTTCAAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTT                                                                                                                                                    <  1:579609/141‑1        TTAATGGTTGTAGATCCATTACTAACTTTTCGAAGTCTTTATCATTTATTGCATTGTTACGTTTGATTGTACTGTCTTGAGTTGTCAAATCGTATTTCAAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTT                                                                                                                                                    <  2:464910/141‑1        TTAATGGTTGTAGATCCATTACTAACTTGTCGAAGTCTTTATCATTTATTGCATTGTTACGTTTGATTGTACTGTCTTGAGTTGTCCAATCGTATTTCAAATATTAAACTAACCCCTCCTATCTAAAATTTAAGGTTAGTT                                                                                                                                                    <  2:89695/141‑1        TTAATGATTGTATATCCATTACTAACTTTTCGAAGTCTTTATCATTTATTGCATTGTTACGTTTGATTGTACTGTCTTGATTTGTCAGATCGTATTTCAAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTT                                                                                                                                                    <  1:276931/141‑1            TGGTTGTAGATCCATTACTAACTTTTCGAAGTCTTTATCATTTATTGCATTGTTACGTTTGATTGTACTGTCTTGAGTTGTCAAATCGTATTTCAAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGATAGTTTAAT                                                                                                                                                >  1:855212/1‑141            TGGTTGTAGATCCATTACTAACTTGTCGGAGTCTTTATCATTTATTGCACTGTTTGGTTTTAGAGGACTGTCTTGAGTTGTCAAATCGTATTTCAAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAAT                                                                                                                                                >  1:933668/1‑141               TTGTAGATCCATTACTAACTTTTCGAAGTCTTTATCATTTATTGCATTGTTACGTTTGATTGTACTGTCTTGAGTTGTCAAATCGTATTTCAAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATT                                                                                                                                             >  2:854916/1‑141               TTGTAGATCCATTACTAACTTTTCGAAGTCTTTATCATTTATTGCATTGTTACGTTTGATTGTACTGTCTTGAGTTGTCAAATCGTATTTCAAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATT                                                                                                                                             >  2:195542/1‑141                   AGATCCATTACTAACTTTTCGAAGTCTTTATCATTTATTGCATTGTTACGTTTGATTGTACTGTCTTGAGTTGTCAAATCGTATTTCAAATATTAAACTAACACCTTCTATCTAAAATTTAAGGTTAGTTTAATATTTtta                                                                                                                                         >  1:51132/1‑138                                                                                                             TATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTTGAAATACGATTTGACAACTCAAGACAGTACAATCAAACGTAACAATGCAATAAATGATAAAGACTTCGAAAAGTTAGTAATGGATCTACAACC                                               >  2:110055/1‑141                                                                                                             TATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTTGAAATACGATTTGACAACTCAAGACAGTACAATCAAACGTAACAATGCAATAAATGATAAAGACTTCGAAAAGTTAGTAATGGATCTACAACC                                               >  1:154233/1‑141                                                                                                               TTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATTTGAAATACGATTTGACAACTCAAGACAGTACAATCAAACGTAACAATGCAATAAATGATAAAGACTTCGAAAAGTTAGTAATGGATCTACAACCAT                                             >  1:441866/1‑141                                                                                                                                                TAGTTTAATATTTGAAATACGATTTGACAACTCAAGACAGTACAATCAAACGTAACAATGCAATAAATGATAAAGACTTCGAAAAGTTAGTAATGGATCTACAACCATTAATTATTCGACGCATCAAAACATTTGGATTTA            <  1:219102/141‑1                                                                                                                                                  GTTTAATATTTGAAATACGATTTGACAACTCAAGACAGTACAATCAAACGTAACAATGCAATAAATGATAAAGACTTCGAAAAGTTAGTAATGGATCTACAACCATTAATTATTCGACGCATGAAAAGATTTGGAGTTAAT          >  2:715347/1‑141                                                                                                                                                  GTTTAATATTTGAAATACGATTTGACAACTCAAGACAGTACAATCAAACGTAACAATGCAATAAATGATAAAGACTTCGAAAAGTTAGTAATGGATCTACAACCATTAATTATTCGACGCATCAAAACATTTGGATTTAAT          >  2:222129/1‑141                                                                                                                                                  GTTTAATATTTGAAATACGATTTGACAACTCAAGACAGTACAATCAAACGTAACAATGCAATAAATGATAAAGACTTCGAAAAGTTAGTAATGGATCTACAACCAGTAATTATTCGACGCATCAAAAAAATTGGAATTAAc          >  2:576067/1‑140                                                                                                                                                      AATATTTGAAATACGATTTGACAACTCAAGACAGTACAATCAAACGTAACAATGCAATAAATGATAAAGACTTCGAAAAGTTAGTAATGGATCTACAACCATTAATTATTCGACGCATCAAAACATTTGGATTTAATCATT      <  1:793937/141‑1                                                                                                                                                       ATATTTGAAATAGGATTTTACAACTCAAGATAGTACAATCAAACGTAACAATGCAATAAATGATAAAGACTTCGAAAAGTTAGTAATGGATCTACAACCATTAATTATTCGACCCAGTTTAATATTTGGATTTAATCATTA     <  2:457432/141‑1                                                                                                                                                          TTTGAAATACGATTTGACAACTCAAGACAGTACAATCAAACGTAACAATGCAATAAATGATAAAGACTTCGAAAAGTTAGTAATGGATCTACAACCATTAATTATTCGACGCATCAAAACATTTGGATTTAATCATTATGA  <  2:191112/141‑1                                                                                                                                                          TTTGAAATACGATTTGACAACTCAAGACAGTACAATCAAACGTAACAATGCAATAAATGATAAAGACTTCGAAAAGTTAGTAATGGATCTACAACCATTAATTATTCGACGCATCAAAACATTTGGATTTAATCATTATGA  <  1:803565/141‑1                                                                                                                                                          TTTGAAATACGATTTGACAACTCAAGACAGGACAATCAAACGTAACAATGCAATAAATGATAAAGACTTCGAAAAGTTAGTAATGGATCTACAACCATTAATTATTCGACGCATCAAAACATTTGGATTTAATCATTATGA  <  2:343148/141‑1                                                                                                                                                                                                                                                                                                        CGAATAATTAATGGTTGTAGATCCATTACTAACTTTTCGAAGTCTTTATCATTTATTGCATTGTTACGTTTGATTGTACTGTCTTGAGTTGTCAAATCGTATTTCAAATATTAAACTAACCCCTTCTATCTAAAATTTAAGGTTAGTTTAATATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/580893‑580739 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ggttagtttaatattTGAAATACGATTTGACAACTCAAGACAGTACAATCAAACGTAACAATGCAATAAATGATAAAGACTTCGAAAAGTTAGTAATGGATCTACAACCATTAATTATTCGACGCATCAAAACATTTGGATTTAATCATTATGA  >  USA300TCH1516_ALE/580788‑580926

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ 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.