New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	5099995 =	22 (0.760)	4 (0.170)	4/214	2.9	19.6%	intergenic (+33/+120)	PP_4488/phhR	hypothetical protein/sigma‑54 dependent transcriptional regulator
	?	NC_002947	5100077 =	15 (0.640)					intergenic (+115/+38)	PP_4488/phhR	hypothetical protein/sigma‑54 dependent transcriptional regulator
Rejected: Frequency below/above cutoff threshold.

GAAGTGCCCAATGTGTGCGAAGTCGTGCCGGCCCGCATGACCTACGAGGACTCCCAGGGCCAGAAGCACATTCTCGAATACCGCGTGATGGGGAACGGCTGCTCCAACGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACAAGGCCGCTCCCACAGATAATGCGCTCAGCCAGAGCACAGCGTATTACCTGTGGGAGCGGCCTTGTGTCGCGAAAGGACTGCAACGCAGTCCCAGGTTCTTTGACCAACAACTAATCCGCCGACTT  >  NC_002947/5099849‑5100129                                                                                                                                                   |                                                                                                                                       gAAGTGCCCAATGTGGGCGAAGTCGTGCCGGCCCGCATGACCTACCAGGACTCCCAGGGCCAGAAGCACATTCTCGAATACCGCGTGATGGGGAACGGCTGCTCCAACGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATcgc                                                                                                                                     <  2:502088/150‑1 (MQ=255)   aGTGCCCAATGTGTGCGAAGTCGTGCCGGCCCGCATGACCTACGAGGACTCCCAGGGCCAGAAGCACATTCTCGAATACCGCGTGATGGGGAACGGCTGCTCCAACGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGa                                                                                                                                   <  1:181344/150‑1 (MQ=255)        ccAATGTGTGCGAAGTCGTGCCGGCCCGCATGACCTACGAGGACTCCCAGGGCCAGAAGCACATTCTCGAATACCGCGTGATGGGGAACGGCTGCTCCAACGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACaa                                                                                                                              >  1:577814/1‑150 (MQ=255)           ttcccagtagtcgggccttgggcaaaagactgggtgtttcgcacacgacaattgccaacaagttgagggattactcgcttaacaagtcggcggattagttgttggtcaaagaacctgggactgcgttgcagtccttTCGCGACACAAGGc                                                                                                                           <  2:127207‑M1/14‑1 (MQ=255)             gtgtgCGAAGTCGTGCCGGCCCGCATGACCTACGAGGACTCCCAGGGCCAGAAGCACATTCTCGAATACCGCGTGATGGGGAACGGCTGCTCCAACGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACAAGGCCg                                                                                                                         >  2:271097/1‑150 (MQ=255)             cccagtagtcgggccttgggcaaaagactgggtgtttcgcacacgacaattgccaacaagttgagggattactcgcttaacaagtcggcggattagttgttggtcaaagaacctgggactgcgttgcagtccttTCGCGACACAAGGCCg                                                                                                                         <  1:379383‑M1/16‑1 (MQ=255)               cagtagtcgggccttgggcaaaagactgggtgtttcgcacacgacaattgccaacaagttgagggattactcgcttaacaagtcggcggattagttgttggtcaaagaacctgggactgcgttgcagtccttTCGCGACACAAGGCCGCt                                                                                                                       >  2:677546‑M1/133‑150 (MQ=255)                tgCGAAGTCGTGCCGGCCCGCATGACCTACGAGGACTCCCAGGGCCAGAAGCACATTCTCGAATACCGCGTGATGGGGAACGGCTGCTCCAACGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACAAgg                                                                                                                            <  2:718175/144‑1 (MQ=255)                tgCGAAGTCGTGCCGGCCCGCATGACCTACGAGGACTCCCAGGGCCAGAAGCACATTCTCGAATACCGCGTGATGGGGAACGGCTGCTCCAACGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACAAgg                                                                                                                            >  1:718175/1‑144 (MQ=255)                    gtcgggccttgggcaaaagactgggtgtttcgcacacgacaattgccaacaagttgagggattactcgcttaacaagtcggcggattagttgttggtcaaagaacctgggactgcgttgcagtccttTCGCGACACAAGGCCGCTCCcac                                                                                                                  >  2:379383‑M1/128‑150 (MQ=255)                       tCGTGCCGGCCCGCATGACCTACGAGGACTCCCAGGGCCAGAAGCACATTCTCGAATACCGCGTGATGGGGAACGGCTGCTCCAACGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACAAGGCCGCTCCCACAGa                                                                                                               <  2:577814/150‑1 (MQ=255)                             cGGCCCGCATGACCTACGAGGACTCCCAGGGCCAGAAGCACATTCTCGAATACCGCGTGATGGGGAACGGCTGCTCCAACGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACAAGGCCGCTCCCACAGATAATgc                                                                                                         <  2:196203/150‑1 (MQ=255)                                                  aCTCCCAGGGCCAGAAGCACATTCTCGAATACCGCGTGATGGGGAACGGCTGCTCCAACGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACAAGGCCGCTCCCACAGATAATGCGCTCAGCCAGCGCACAGCGtc                                                                                    <  2:11013/150‑2 (MQ=255)                                                     cccAGGGCCAGAAGCACATTCTCGAATACCGCGTGATGGGGAACGGCTGCTCCAACGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACAAGGCCGCTCCCACAGATAATGCGCTCAGCCAGAGCACAGCGTATTa                                                                                 >  1:113118/1‑150 (MQ=255)                                                         gacaattgccaacaagttgagggattactcgcttaacaagtcggcggattagttgttggtcaaagaacctgggactgcgttgcagtccttt                                                                                                                                        <  1:463936‑M1/1‑1 (MQ=255)                                                         gacaattgccaacaagttgagggattactcgcttaacaagtcggcggattagttgttggtcaaagaacctgggactgcgttgcagtccttt                                                                                                                                        >  2:463936‑M1/91‑91 (MQ=255)                                                            ccAGAAGCACATTCTCGAATACCGCGTGATGGGGAACGGCTGCTCCAACGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACAAGGCCGCTCCCACAGATAATGCGCTCAGCCAGAGTACAGCGTATTACCTGTgg                                                                          >  1:293842/1‑150 (MQ=255)                                                                aaGCACATTCTCGAATACCGCGTGATGGGGAACGGCTGCTCCAACGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACAAGGCCGCTCCCACAGATAATGCGCTCAGCCAGAGca                                                                                           <  2:32824/129‑1 (MQ=255)                                                                aaGCACATTCTCGAATACCGCGTGATGGGGAACGGCTGCTCCAACGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACAAGGCCGCTCCCACAGATAATGCGCTCAGCCAGAGca                                                                                           >  1:32824/1‑129 (MQ=255)                                                                        gttgagggattactcgcttaacaagtcggcggattagttgttggtcaaagaacctgggactgcgttgcagtccttTCGCGACACAAGGCCGCTCCCACAGATAATGCGCTCAGCCAGAGCACAGCGTATTACCTGTgg                                                                          <  1:270686‑M1/63‑1 (MQ=255)                                                                        gttgagggattactcgcttaacaagtcggcggattagttgttggtcaaagaacctgggactgcgttgcagtccttTCGCGACACAAGGCCGCTCCCACAGATAATGCGCTCAGCCAGAGCACAGCGTATTACCTGTgg                                                                          >  2:270686‑M1/76‑138 (MQ=255)                                                                          tcGAATACCGCGTGATGGGGAACGGCTGCTCCAACGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACAAGGCCGCTCCCACAGATa                                                                                                             <  1:557022/101‑1 (MQ=255)                                                                          tcGAATACCGCGTGATGGGGAACGGCTGCTCCAACGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACAAGGCCGCTCCCACAGATa                                                                                                             >  2:557022/1‑101 (MQ=255)                                                                           gagggattactcgcttaacaagtcggcggattagttgttggtcaaagaacctgggactgcgttgcagtccttTCGCGACACAAGGCCGCTCCCACAGATAATGCGCTCAGCCAGAGCACAGCGTATTACCTGTGGGAg                                                                       >  1:99041‑M1/73‑138 (MQ=255)                                                                           gagggattactcgcttaacaagtcggcggattagttgttggtcaaagaacctgggactgagttgcagtccttTCGCGACACAAGGCCGCTCCCACAGATAATGCGCTCAGCCAGAGCACAGCGTATTACCTGTGGGAg                                                                       <  2:99041‑M1/66‑1 (MQ=255)                                                                            gAATACCGCGTGATGGGGAACGGCTGCTCCAACGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACAAGGCCGCTCCCACAGATAATGCGCTCAGCCAGAGCACAGCGTATTACCTGTGGGAGCGGCCTTGTGTcg                                                          <  2:113118/150‑1 (MQ=255)                                                                                                          aaCGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACAAGGCCGCTCCCACAGATAATGCGCTCAGCCAGAGCACAGCGTATTAc                                                                                <  2:356565/98‑1 (MQ=255)                                                                                                          aaCGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACAAGGCCGCTCCCACAGATAATGCGCTCAGCCAGAGCACAGCGTATTAc                                                                                >  1:356565/1‑98 (MQ=255)                                                                                                           aCGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACAAGGCCGCTCCCACAGATAATGCGCTCAGCCAAAGCACAAACATTTACCTGTGGGAGCGGCCTTGTGTCGCGAAAGGACTGCAACGCAGTCCCAGGTTCtt                           >  2:206486/1‑150 (MQ=255)                                                                                                                   tACCTTGGAGTCGGGGGCCCTGCGGGCCCCTATCGCGACACAAGGCCGCTCCCACAGATAATGCGCTCAGCCAGAGCACAGCGTATTACCTGTGGGAGCGGCCTTGTGTCGCGAAAGGACTGCAACGCAGTCCCAGGTTCTTTGACcaac                   <  1:510424/150‑1 (MQ=255)                                                                                                                                   gCCCTGCGGGCCCCTATCGCGACACAAGGCCGGTCCCACAGATAATGCGCTCAGCCAGAGCACCGCGTATTACCTGTGGGAGCGGCCTTGTGTCGCGAAAGGACTGCAACGCAGTCCCAGGTTCTTTGACCAACAACTAATCCGCCGACt   >  1:213557/1‑150 (MQ=255)                                                                                                                                    cccTGCGGGCCCCTATCGCGACACAAGGCCGCTCCCACAGATAATGCGCTCAGCCAGAGTACAGCGTATTACCTGTGGGAGCGGCCTTGTGTCGCGAAAGGACTGCAACGCAGTCCCAGGTTCTTTGACCAACAACTAATCCGCCGACtt  <  2:293842/150‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                       GAAGTGCCCAATGTGTGCGAAGTCGTGCCGGCCCGCATGACCTACGAGGACTCCCAGGGCCAGAAGCACATTCTCGAATACCGCGTGATGGGGAACGGCTGCTCCAACGGCTGATACCTTGGAATCGGGGGCCCTGCGGGCCCCTATCGCGACACAAGGCCGCTCCCACAGATAATGCGCTCAGCCAGAGCACAGCGTATTACCTGTGGGAGCGGCCTTGTGTCGCGAAAGGACTGCAACGCAGTCCCAGGTTCTTTGACCAACAACTAATCCGCCGACTT  >  NC_002947/5099849‑5100129

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