New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	4963771 =	26 (0.490)	3 (0.060)	3/240	NT	10.4%	intergenic (‑117/+111)	fleS/fleQ	two‑component system sensor histidine kinase FleS/transcriptional regulator FleQ
	?	NC_002947	4963837 =	27 (0.540)					intergenic (‑183/+45)	fleS/fleQ	two‑component system sensor histidine kinase FleS/transcriptional regulator FleQ

TGTGTTGCCAGCGGTGTAGCAATAGCCGTGCCGGAGATGGGGGTTTGGGTTTGACGTAGGATTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTCAGCCGCGCGCG  >  NC_002947/4963690‑4963985                                                                                                                                                     |                                                                                                                                                     agccgccagggcggtgaggaccaggcggaggattgatgtttgggctgggtgttcgccttgggggttgcgtttgggcggggtGTTCGCCGTGAGTTTTGTTGTGCCGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCTAaca                                                                                                                                                      >  6:338042‑M1/82‑148 (MQ=255)                                         gggtttgggtttGACGTAGGATTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGC‑GGAGATCGGGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCa                                                                                                              >  2:94454/1‑148 (MQ=255)                                          ggtttgggtttgACGTAGGATTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGC‑GGAGATCGGGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCaaa                                                                                                            <  1:94454/149‑1 (MQ=255)                                            tttgggtttgACGTAGGATTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACGCCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAg                                                                                                                  <  4:68612/141‑1 (MQ=255)                                            tttgggtttgACGTAGGATTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACGCCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAg                                                                                                                  >  3:68612/1‑141 (MQ=255)                                                ggtttgACGTAGGATTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCaa                                                                                                      >  7:46329/1‑149 (MQ=255)                                                  tttgACGTAGGATTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAAtc                                                                                                    <  7:210872/149‑1 (MQ=255)                                                  tttgACGTAGGATTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAAt                                                                                                     >  2:270584/1‑148 (MQ=255)                                                              ttGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTCTTGTTGTGCCGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTc                                                                                        >  1:196371/1‑149 (MQ=255)                                                                  gTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGCGGGTGAACGCGCGCCGCCCAAACAAAACCCTCAAGGCGAACCCCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCGGGTCCt                                                                                      >  1:248058/1‑148 (MQ=255)                                                                  gTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCCGCCCAAACATCAATCCTCCGCCGGGTCCtaa                                                                                    >  1:240797/1‑147 (MQ=255)                                                                  gTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCa                                                                                    >  8:16833/1‑149 (MQ=255)                                                                   ttAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCAc                                                                                   >  5:133833/1‑149 (MQ=255)                                                                    tAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCAcc                                                                                  >  7:303573/1‑149 (MQ=255)                                                                             gaAGGGTTCGCCGTGAGTTTTGTTGTGCCGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTggcg                                                                         >  8:176928/1‑149 (MQ=255)                                                                                gggTTCGCCGTGAGTTTTGTTGTGCCGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCt                                                                      >  2:178637/1‑149 (MQ=255)                                                                                  tgttagccttgaggtttttgtttgggcggcgctcgatctccgcggcacaacaaaactcacggcgaacACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCt                                                                      >  6:338042‑M2/68‑148 (MQ=255)                                                                                    ttcgccttgaggtttttgtttgggcggcgctcgatctccgcggcacaacaaaactcacggcgaacACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCAt                                                                   >  1:80376‑M2/66‑149 (MQ=255)                                                                                     CGCCGTGAGTTTTGTTGTGCCGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATg                                                                  >  8:303573‑M1/1‑148 (MQ=255)                                                                                              ttttGTTGTGCCGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACttcc                                                        >  2:291907/1‑147 (MQ=255)                                                                                               gtttttgtttgggcggcgctcgatctccgcggcacaacaaaactcacggcgaacACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTgc                                                        <  5:338042‑M2/95‑1 (MQ=255)                                                                                                      tgCCGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTtc                                                <  2:196371/149‑1 (MQ=255)                                                                                                        ccGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTtctc                                              <  7:16833/149‑1 (MQ=255)                                                                                                        ccGC‑GGAGATCGAGCGCCGACCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCGCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTtctc                                              <  7:176928/149‑1 (MQ=255)                                                                                                               agaTCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAg                                        <  1:178637/149‑1 (MQ=255)                                                                                                                    gAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGggtg                                    <  8:46329/148‑1 (MQ=255)                                                                                                                          cgccCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACACAACCCCCAAGGCGAACACACAGCCCAAACAAAAATCATCCGCCAGGTCCTAACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGc                             >  8:52499/1‑149 (MQ=255)                                                                                                                             ccAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAgg                                       >  2:308696/1‑136 (MQ=255)                                                                                                                             ccAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAgg                                       <  1:308696/136‑1 (MQ=255)                                                                                                                             ccAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGaa                          <  6:133833/149‑1 (MQ=255)                                                                                                                                   aaaaaCCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGa                           >  6:127320/1‑142 (MQ=255)                                                                                                                                   aaaaaCCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGa                           <  5:127320/142‑1 (MQ=255)                                                                                                                                           cAAGGCGAACTCCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGc                             <  5:265922/132‑1 (MQ=255)                                                                                                                                                     acCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTCAGCcgcgcgcg  >  7:238832/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                     TGTGTTGCCAGCGGTGTAGCAATAGCCGTGCCGGAGATGGGGGTTTGGGTTTGACGTAGGATTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGC‑GGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAGCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTCAGCCGCGCGCG  >  NC_002947/4963690‑4963985

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.