New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	1846959 =	71 (1.180)	5 (0.120) +TTGCGCTTGTGGATGAGGTTGCCGTTGCATGTGCCGGCCT	5/186	NT	9.2%	coding (1250/1377 nt)	pfeS‑II	histidine kinase
	?	NC_002947	2435235 =	NA (NA)					intergenic (+82/‑222)	PP_2133/PP_2134	hypothetical protein/transposase

GCGCAACCCGCGTTTGCCATTCTGCGCCCACAAGGTGCCGCCCTGGCGCTGGATGGC‑ACTGCGGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_002947/1847023‑1846959 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAGGAGGAGGGCCATAACTCGCTTCTGACTGTTCGCGCAGTACAGACCG‑TAGGAGAAATCACCCCTCCTCCTTTCAACACCCAAGCGCCGATAAGGAATGCCT  >  NC_002947/2435235‑2435376                                                                   ||||||||||||||||||||||||||||||||||||||||                                                                                                                                                GCGCAACCCGCGTTTGCCATTCTGCGCCCACAAGGTGCCGCCCTGGCGCTGGATGGC‑ACTGCGGGTTGCGCTTGTGGATGAGGTTGCCGTTGCATGTGCCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAG                                                                                                       >  8:298702/1‑147       CCCGCGTTTGCCATTCTGCGCCCACAAGGTGCCGCCCTGGCGCTGGATGGC‑ACTGCGGGTTGCGCTTGTGGATGAGGTTGCCGTTGCATGTGCCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAGGAGGAGGG                                                                                               >  1:105705/1‑149         CGCGTTTGCCATTCTGCGCCCACAAGGTGCCGCCCTGGCGCTGGATGGC‑ACTGCGGGTTGCGCTTGTGGATGAGGTTGCCGTTGCATGTGCCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAGGAGGAGGGCC                                                                                             <  2:105705/149‑1             TTTGCCATTCTGCGCCCACAAGGTGCCGCCCTGGCGCTGGATGGCAAACGCGGGTTGCGCTTGTGGATGAGGTTGCCGTTGCATGTGCCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAGGAGGAGGGCCAT                                                                                           >  5:298158/1‑148                         CGCCCACAAGGTGCCGCCCTGGCGCTGGATGGCAAACGCGGGTTGCGCTTGTGGATGAGGTTGCCGTTGCATGTGCCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAGGAGGAGGGCCATAACTCGCTTCTGA                                                                              <  6:298158/149‑1                                                              GCGGGTTGCGCTTGTGGATGAGGTTGCCGTTGCATGTGCCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAGGAGGAGGGCCATAACTCGCTTCTGACTGTTCGCGCAGTACAGACCG‑TAGGAGAAATCACCCC                                        >  3:299338/1‑149                                                                      CGCTTGTGGATGAGGTTGCCGTTGCATGTGCCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAGGAGGAGGGCCATAACTCGCTTCTGACTGTTCGCGCAGTACAGACCG‑TAGGAGAAATCACCCCTCCTCCTT                                <  4:183992/149‑1                                                                        CTTGTGGATGAGGTTGCCGTTGCATGTGCCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAGGAGGAGGGCCATAACTCGCTTCTGACTGTTCGCGCAGTACAGACCG‑TAGGAGAAATCACCCCTCCTCCTTTC                              <  7:298702/149‑1                                                                               ATGAGGTTGCCGTTGCATGTGCCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAGGAGGAGGGCCATAACTCGCTTCTGACTGTTCGCGCAGTACAGACCG‑TAGGAGAAATCACCCCTCCTCCTTTCAACACCC                       <  1:128509/149‑1                                                                               ATGAGGTTGCCGTTGCATGTGCCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAGGAGGAGGGCCATAACTCGCTTCTGACTGTTCGCGCAGTACAGACCG‑TAGGAGAAATCACCCCTCCTCCTTTCAACACCC                       <  8:34395/149‑1                                                                                  AGGTTGCCGTTGCATGTGCCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAGGAGGAGGGCCATAACTCGCTTCTGACTGTTCGCGCAGTACAGACCG‑TAGGAGAAATCACCCCTCCTCCTTTCAACACCCAA                     <  1:142101/148‑1                                                                                   GGTTGCCGTTGCATGTGCCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAGGAGGAGGGCCATAACTCGCTTCTGACTGTTCGCGCAGTACAGACCG‑TAGGAGAAATCACCCCTCCTCCTTTCAACACCCAAGC                   >  7:283838/1‑149                                                                                       GCCGTTGCATGTGCCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAGGAGGAGGGCCATAACTCGCTTCTGACTGTTCGCGCAGTACAGACCG‑TAGGAGAAATCACCCCTCCTCCTTTCAACACCCAAGCGCC                <  4:299338/148‑1                                                                                               ATGTGCCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAGGTCTTGCAGGGAGGACGAGGGACATAACTCGCTTCTGACTGTTCCCGCAGTACAGACCG‑TAGGAGAAATCACCCCTCCTCCTTTCAACACCCAAGCGCCGATAAGGAA       <  2:173348/149‑1                                                                                               ATGTGCCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAGGAGGAGGGCCATAACTCGCTTCTGACTGTTCGCGCAGTACAGACCGCTAGGAGAAATCACCCCTCCTCCTTTCAACACCCAAGCGCCGATAAGGA        <  1:274847/149‑1                                                                                               ATGTGCCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAGGAGGAGGGCCATAACTCGCTTCTGACTGTTCGCGCAGTACAGACCG‑TAGGAGAAATCACCCCTCCTCCTTTCAACACCCAAGCGCCGATAAGGAA       <  3:8728/149‑1                                                                                               ATGTGCCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAGGAGGAGGGCCATAACTCGCTTCTGACTGTTCGCGCAGTACAGACCG‑TAGGAGAAATCACCCCTCCTCCTTTAACCACCCAAGCGCCGATAAGGAA       >  1:196944/1‑149                                                                                                TGTGCCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAAGACTTGAAGGGAGGAGGAGGGCCATAACTCGCTTCTGACTGTTCGCGCAGTACAGACCG‑TAGGAGAAATCACCCCTCCTCCTTTCAACACCCAAGCGCCGATAAGGAAT      >  3:256073/1‑149                                                                                                   GCCGGCCTCTTCGCCGGAAAACCCCCTTGTATGGAAGGACTTGAAGGGAGGAGGAGGGCCATAACTCCCTTCTGACTGTTCGCGCAGTACAGACCG‑TAGGAGAAAACACACCTCCACCTAAAAACACACAAGCGCCCATAACGAATGCC   >  2:361623/1‑149                                                                                                    CCGGCCTCTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAGGAGGAGGGCCATAACTCGCTTCTGACTGTTCGCGCAGTACAGACCG‑TAGGAGAAATCACCCCTCCTCCTTTCAACACCCAAGCGCCGATAAGGAATGCCT  <  7:129921/149‑1                                                                   ||||||||||||||||||||||||||||||||||||||||                                                                                                                                                GCGCAACCCGCGTTTGCCATTCTGCGCCCACAAGGTGCCGCCCTGGCGCTGGATGGC‑ACTGCGGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_002947/1847023‑1846959 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTTCGCGGGTAAACCCGCTTGTATGGTAGGACTTGAAGGGAGGAGGAGGGCCATAACTCGCTTCTGACTGTTCGCGCAGTACAGACCG‑TAGGAGAAATCACCCCTCCTCCTTTCAACACCCAAGCGCCGATAAGGAATGCCT  >  NC_002947/2435235‑2435376

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ 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.