New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4321860 =	48 (1.470)	4 (0.130)	4/258	3.4	8.0%	coding (563/726 nt)	phnF	putative DNA‑binding transcriptional regulator of phosphonate uptake and biodegradation
	?	NC_000913	4321892 =	46 (1.470)					coding (531/726 nt)	phnF	putative DNA‑binding transcriptional regulator of phosphonate uptake and biodegradation
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAGGTGGATGACG  >  NC_000913/4321751‑4322039                                                                                                                                              |                                                                                                                                                    cTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCg                                                                                                                                               <  5:13440/148‑1 (MQ=255)  tCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGt                                                                                                                                             >  3:23857/1‑149 (MQ=255)          gctgctTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTcgc                                                                                                                                     >  7:71056/1‑149 (MQ=255)           ctgctTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTcgcg                                                                                                                                    >  1:10572/1‑149 (MQ=255)              ctTTCACCGTCACGGTGGTTAAGGGGGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCa                                                                                                                                  <  5:133853/148‑1 (MQ=255)                    ccGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATc                                                                                                                           <  8:71056/149‑1 (MQ=255)                      gTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGt                                                                                                                         <  1:50658/149‑1 (MQ=255)                       tCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTg                                                                                                                        <  4:23857/149‑1 (MQ=255)                           ggtggtTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGAGTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGc                                                                                                                    >  4:104724/1‑149 (MQ=255)                                              gcacAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGtt                                                                                                 >  4:57764/1‑149 (MQ=255)                                                acaGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTg                                                                                                >  7:35838/1‑148 (MQ=255)                                                 cagcagCGGCGACATATTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCa                                                                                              <  3:88053/149‑1 (MQ=255)                                                  agcagcGGCGACATATTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGc                                                                                                                <  2:159146/130‑1 (MQ=255)                                                  agcagcGGCGACATATTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGc                                                                                                                >  1:159146/1‑130 (MQ=255)                                                  agcagcGGCGACATATTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAg                                                                                             >  4:27772/1‑149 (MQ=255)                                                               tatTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAgg                                                                                >  4:45477/1‑149 (MQ=255)                                                                 ttCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCCGCGAGCCGCTGTCGAAGCGTTGCCGCGTCGGCCAGAGGGt                                                                              >  4:124752/1‑149 (MQ=255)                                                                    gggATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAg                                                                           <  1:160695/149‑1 (MQ=255)                                                                    gggATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAg                                                                           >  5:47068/1‑149 (MQ=255)                                                                     ggATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTc                                                                                         >  1:127923/1‑134 (MQ=255)                                                                     ggATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTc                                                                                         >  1:130102/1‑134 (MQ=255)                                                                     ggATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTc                                                                                         <  2:127923/134‑1 (MQ=255)                                                                     ggATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTc                                                                                         <  2:130102/134‑1 (MQ=255)                                                                        tttCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTcc                                                                       >  4:85891/1‑149 (MQ=255)                                                                        tttCAAGACGCTGGCACTCTTTGGCATGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTAGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGAcc                                                                       >  6:88149/1‑149 (MQ=255)                                                                          tCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCcgc                                                                     >  1:39246/1‑149 (MQ=255)                                                                                cGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAagta                                                               <  2:10572/149‑1 (MQ=255)                                                                                cGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGGCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAagta                                                               <  3:27772/149‑1 (MQ=255)                                                                                  cTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCTTCGGCCAGAGTGTGAGGTCCGCGAagtagt                                                             <  5:88149/149‑1 (MQ=255)                                                                                   tGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTg                                                            >  3:80792/1‑149 (MQ=255)                                                                                     gCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTg                                                            <  8:35838/147‑1 (MQ=255)                                                                                     gCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTg                                                            <  3:45477/147‑1 (MQ=255)                                                                                     gCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAACTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGt                                                          <  7:97987/149‑1 (MQ=255)                                                                                       aCTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTc                                                         >  6:39103/1‑148 (MQ=255)                                                                                        ctctTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGc                                                                                               <  4:106186/109‑1 (MQ=255)                                                                                        ctctTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGc                                                                                               >  3:106186/1‑109 (MQ=255)                                                                                           tttGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGAt                                                      <  2:39246/147‑1 (MQ=255)                                                                                                         ggcgggcgCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGGGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACg                                      >  8:40405/1‑149 (MQ=255)                                                                                                          gcgggcgCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAg                                                                           >  5:63407/1‑111 (MQ=255)                                                                                                          gcgggcgCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAg                                                                           <  6:63407/111‑1 (MQ=255)                                                                                                           cgggcgCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAgg                                                                                >  1:64048/1‑105 (MQ=255)                                                                                                           cgggcgCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAgg                                                                                <  2:64048/105‑1 (MQ=255)                                                                                                             ggcgCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCCGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGt                                  >  7:123832/1‑149 (MQ=255)                                                                                                               cgcTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTg                                <  4:80792/149‑1 (MQ=255)                                                                                                                         cgTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCa                      <  6:47068/149‑1 (MQ=255)                                                                                                                          gTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGGGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAg                     <  3:124752/149‑1 (MQ=255)                                                                                                                                         agcgcaATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAGGTGGa       <  4:18408/148‑1 (MQ=255)                                                                                                                                           cgcaATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCcgcg                                                                    <  4:35487/85‑1 (MQ=255)                                                                                                                                           cgcaATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCcgcg                                                                    >  3:35487/1‑85 (MQ=255)                                                                                                                                            gcaATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAGGTGGATGAc   <  3:104724/149‑1 (MQ=255)                                                                                                                                             caATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAGGTGGATGACg  >  6:105481/1‑149 (MQ=255)                                                                                                                                              |                                                                                                                                                    CTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAGGTGGATGACG  >  NC_000913/4321751‑4322039

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.