New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 5545666	NA (NA)	12 (0.220)	11/250	NT	31.3%	intergenic (‑806/+71)	rpsF/rlmB	30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB
	?	NC_002947	5621244 =	27 (0.490)					coding (20/774 nt)	PP_4939	hypothetical protein

CTGACCTACCCGGATCAGTCGGCGAATGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATctc‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/5545551‑5545666 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTCTCA‑TTTGAAAAGCGCACCGGATTCCCTCCGCATTACGACTATCGGCCTTCAACAACCCGCTCCTGGGCGTGAAAGCTCTTGTTTAGATGCCCAGCTTCAGACGCA  >  NC_002947/5621244‑5621351                                                                                                                                                                                                                                   CTGACCTACCCGGATCAGTCGGCGAATGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCTCA‑TTTGAAAAGCGCACCGGATTCCCTCCG                                                                             <  3:29064/149‑1     CCTACCCGGATCAGTCGGCGAATGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCTCA‑TTTGAAAAGCGCACCGGATTCCCTCCGCAT                                                                          >  7:301163/1‑148                     GGCGAATGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCTCA‑TTTGAAAAGCGCACCGGATTCCCTCCGCATTACGACTATCGGCCTT                                                          >  4:28265/1‑148                                     GATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCTCA‑TTTGAAAAGCGCACCGGATTCCCTCCGCATTACGACTATCGGCCTTCAACAACCCGCTCCTGG                                         <  2:28844/149‑1                                        CTCGATGTCAGTGCAGATCTGACGTCATGGGCATCGTGTTTGCTTTTCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCTCA‑TTTGAAAAGCGCACCGGATTCCCTCCGCATTACGACTATCGGCCTTGAACAAGCCGCTCCTGGGC                                       <  2:157061/148‑1                                           GATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCTCA‑TTTGAAAAGCGCACCGGATTCCCTCCGCATTACGACTATCGGCCTTCAACAACCCGCTCCTGGGCGTG                                    >  4:319353/1‑148                                            ATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCTCA‑TTTGAAAAGCGCACCGGATTCCCTCCGCATTACGACTATCGGCCTTCAACAACCCGCTCCTGGGCGTGAA                                  <  3:28265/149‑1                                                               GTCATGCGCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCTCA‑TTTGAAAAGCGCACCGGATTCCCTCCGCATTACGACTATCGGCCTTCAACAACCCGCTCCTGGGCGTGAAAGCTCTTGTTTAGATGCCC               <  3:319353/149‑1                                                                  ATGCGCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCTCA‑TTTGAAAAGCGCACCGGATTCCCTCCGCATTACGACTATCGGC                                                             >  8:262578/1‑100                                                                            TGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCTCAGTTTGAAAAGCGCACCGGATTCCCTCCGCATTACGACTATCGGCCTTCAACAACCCGCTCCTGGGCGTGAAAGCTCTTGTTTAGATGCCCAGCTTCAGACG    >  1:259372/1‑148                                                                            TGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCTCA‑TTTGAAAAGCGCACCGGATTCCCTCCGCATTACGACTATCGGCCTTCAACAACCCGCTCCTGGGCGTGAAAGCTCTTGTTTAGATGCCCAGCTTCAGACG    >  5:272321/1‑147                                                                              TTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCTCA‑TTTGAAAAGCGCACCGGATTCCCTCCGCATTACGACTATCGGCCTTCAACAACCCGCTCCTGGGCGTGAAAGCTCTTGTTTAGATGCCCAGCTTCAGACGCA  <  8:301163/147‑1                                                                                                                                                                                                                                   CTGACCTACCCGGATCAGTCGGCGAATGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATctc‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/5545551‑5545666 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTCTCA‑TTTGAAAAGCGCACCGGATTCCCTCCGCATTACGACTATCGGCCTTCAACAACCCGCTCCTGGGCGTGAAAGCTCTTGTTTAGATGCCCAGCTTCAGACGCA  >  NC_002947/5621244‑5621351

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.