New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 20563	NA (NA)	9 (0.350)	9/266	NT	90.1%	noncoding (1/768 nt)	IS1	repeat region
	?	CP009273	1503915 =	1 (0.040)					noncoding (755/1748 nt)	IS609	repeat region

CGGGCTGTTGCCCGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCTTTTGACTATCTGGCAACCGGCAGTGTGTTCTCTCACGCATCACAAAAGCAGC  >  CP009273/20297‑20757                                                                                                                                                                                                                                                                           |                                                                                                                                                                                                   cGGGCTGTTGCCCGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTCAATCAGTAAGTTGGCAGCATCACCTACCTCac                                                                                                                                                                                            >  1:1649/1‑274 (MQ=17)   gtgggtggCCCGGCATCCAACGCCATTCATGGCCATATCATTGATTTTCTGGTGCGTAACGGGGTGAGAAGCGGTGTAAGTGAACTGAAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAAt                                                                                                                                                                                           <  2:68151/267‑1 (MQ=12)   ggCTGTTGCCCGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAACATCACCAACCCCAAt                                                                                                                                                                                           >  1:68151/1‑274 (MQ=14)            ccGGCATCCAACGCCATTCATTGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCGATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCa                                                                                                                                                                                             <  1:271561/263‑1 (MQ=17)                                 ggCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGANAGCAGAGANAGCGCTGATGTCAGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTAAATGTGTGTCACAATATCCATATTCTTTGTgggg                                                                                                                                                            <  1:341156/275‑1 (MQ=255)                                  gtcATATCAATGATTTTCTGGTGCGTACCGGGTTTAGATGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCATAGATAGCGCTGATGTCCGGCGGTGCGTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTggggg                                                                                                                                                           <  2:465421/273‑1 (MQ=255)                                      tatCAATGATTTTCTGGTGAGTACCCGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGACAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTCGCTGAACAGGAGACCCAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCACACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTATAACACAAAAACCAAAATCTTTGAGAGGGAgc                                                                                                                                                        >  1:425449/1‑273 (MQ=11)                                                                                                                tGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATCTCCATATTCTTTGTGGAGGAGTCGGGAGATTGAGGAAATATTCTTGTTAAGAATGTATAAGCCGATGGTTATAGGCTTGTTAAGCAANGacgcgcgt                                                                             >  2:202648/1‑268 (MQ=18)                                                                                                                 gagaGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCa                                                                            <  1:182304/275‑1 (MQ=255)                                                                                                                   gagCAGAGATAGCGCTGATGTCCCGCGGTGCTCTTGCCTTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATCGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGt                                                                                                                                           <  1:275809/210‑1 (MQ=255)                                                                                                                          gaTAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTGCGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCGATATTCTTTGTGNGGGAGTCTNGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTTTACGATTCTTAAGCCAAGAAGAATTCAGAAAgaaaa                                                                   >  1:346937/1‑271 (MQ=255)                                                                                                                          gaTAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAGAAGTNTAGATAATACa                                                                   >  2:50495/1‑275 (MQ=255)                                                                                                                              gcgcTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACTCTAAATCAGTAAGTTGGCAGCATCacctac                                                                                                                                                                                                 >  2:435217/1‑145 (MQ=14)                                                                                                                               cgcTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGc                                                              >  2:123891/1‑275 (MQ=255)                                                                                                                                  tGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACTCTAAATCAGTAAGTTGGCAGCATCACCTACCTCa                                                                                                                                                                                             <  1:435226/145‑1 (MQ=21)                                                                                                                                   gATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGcc                                                                                        >  2:419798/1‑245 (MQ=255)                                                                                                                                       tCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTTTACGATTCTTAAGCCACGa                                                                                    <  1:419807/245‑1 (MQ=255)                                                                                                                                         cggcggTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAAtgt                                                                                                                                                                                         >  1:260253/1‑142 (MQ=38)                                                                                                                                             ggTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTAt                                                                                                                                                                                     <  2:260249/142‑1 (MQ=40)                                                                                                                                                                accaccCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGcc                                                                                        >  1:228258/1‑216 (MQ=255)                                                                                                                                                                            gTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCacctac                                                                                                                                                                                                 >  2:285698/1‑99 (MQ=32)                                                                                                                                                                               gCTGAACAGGAGGGACAGCTGATAGAAAAAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCacctacct                                                                                                                                                                                               >  1:386722/1‑98 (MQ=21)                                                                                                                                                                                cTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCa                                                                                                                                                                                             <  1:285702/99‑1 (MQ=37)                                                                                                                                                                                   aaCAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAAt                                                                                                                                                                                           <  2:386714/98‑1 (MQ=39)                                                                                                                                                                                            gACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCTTTTGACTATCTGGCAACCGGCAGTGTGTTCTCTCACGCATCACAAAagcagc  <  1:123892/274‑1 (MQ=255)                                                                                                                                                                                             aCAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCaa                                                                                                                                                                                            >  2:45084/1‑87 (MQ=39)                                                                                                                                                                                             aCAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCAGATGGTTCTACGATTCTTAAGCCACGAAGAGtt                                                                              >  1:405745/1‑197 (MQ=255)                                                                                                                                                                                                 cTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAAtgtg                                                                                                                                                                                        <  1:45084/87‑1 (MQ=255)                                                                                                                                                                                                 cTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGa                                                                          <  2:405736/197‑1 (MQ=255)                                                                                                                                                                                                                                       ccATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCTTTTGACTATCTGGCAACCGGCAGTGTGTTCTCTCAc                  >  2:226488/1‑215 (MQ=255)                                                                                                                                                                                                                                                    aaTCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATc                                                                                                                                                                                    >  1:280925/1‑40 (MQ=255)                                                                                                                                                                                                                                                    aaTCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGtt                                                                                                        >  2:523798/1‑116 (MQ=255)                                                                                                                                                                                                                                                        aGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACaa                                                                                                                                                                                <  2:280921/40‑1 (MQ=255)                                                                                                                                                                                                                                                        aGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTAc                                                                                                    <  1:523808/116‑1 (MQ=255)                                                                                                                                                                                                                                                          tAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAAt                                                                                                                        >  1:411088/1‑94 (MQ=255)                                                                                                                                                                                                                                                          tAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGaa                                                                                   >  1:222445/1‑131 (MQ=255)                                                                                                                                                                                                                                                              ttGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTAt                                                                                                                    <  2:411079/94‑1 (MQ=255)                                                                                                                                                                                                                                                              ttGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGt                                                                               <  2:222442/131‑1 (MQ=255)                                                                                                                                                                                                                                                                      aTCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTg                                                                                                                                                     >  1:491779/1‑53 (MQ=255)                                                                                                                                                                                                                                                                        cACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGtt                                                                              >  2:500221/1‑122 (MQ=255)                                                                                                                                                                                                                                                                          cctacctCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGgaga                                                                                                                                                 <  2:491770/53‑1 (MQ=255)                                                                                                                                                                                                                                                                           |                                                                                                                                                                                                   CGGGCTGTTGCCCGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCTTTTGACTATCTGGCAACCGGCAGTGTGTTCTCTCACGCATCACAAAAGCAGC  >  CP009273/20297‑20757

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ 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.