New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	3274911 =	34 (1.280)	3 (0.120)	3/264	NT	8.4%	pseudogene (482/555 nt)	agaA	pseudogene, N‑acetylgalactosamine‑6‑phosphate deacetylase fragment; putative N‑acetylgalactosamine‑6‑phosphate deacetylase
	?	CP009273	3274929 =	33 (1.300)					pseudogene (500/555 nt)	agaA	pseudogene, N‑acetylgalactosamine‑6‑phosphate deacetylase fragment; putative N‑acetylgalactosamine‑6‑phosphate deacetylase

CAGTGCGCAATATGGTCGAGTTGACGGGCGTAACGCCTGCGGAAGCCATCCATATGGCGTCGCTGCATCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATCTGTGCAGCGGTGTCGGATGCGAC  >  CP009273/3274785‑3275072                                                                                                                                                 |                                                                                                                                                ccgggcgcAATACGGTCGAGTGCGCGGGGGTAACGCTTGCGGAAGTCATCCATATGGCGTCGCTGCAGCCGGCGCGAATGCTGGGTGTTGATGGTGCTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGc                                                                                                                                             <  2:108728/145‑1 (MQ=255)    tGCGCAATATGGGCGAGTGGACGGGCGTAACGCCTGCGGAAGCCATCCATATGGCGTCGCTGCATCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCggg                                                                                                                                          <  1:219037/149‑1 (MQ=255)    gagaccaaagcgaaagaaaaagaaaggccttacgggggaagtgaaggcccaataaaggagcaaactatcaaaacgaagctaattgaccctgaatccagatttgttgcacatgtagcccgctatCCAGCGTCGTTGCGCTGGATAGCggg                                                                                                                                          >  2:260182‑M1/124‑149 (MQ=255)                tCGAGTTGACGGGCGTAACGCCTGCGGAAGCCATCCATATGGCGTCGCTGCATCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGcaa                                                                                                                              >  2:393501/1‑149 (MQ=255)                              gtaatcccTGGGGAAGCCATCCAGGTGGCGTCGCCGCCTCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCa                                                                                                                <  2:150868/143‑1 (MQ=255)                                    ccTGCGGAAGCCATCCATATGGCGTCGCTGCATCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCa                                                                                                          <  1:396074/149‑1 (MQ=255)                                    ccTGCGGAAGCCATCCATATGGCGTCGCTGCATCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCa                                                                                                          <  1:383377/149‑1 (MQ=255)                                     cTGCGGAAGCCATCCATATGGCGTCGCTGCATCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCaa                                                                                                         >  2:356192/1‑149 (MQ=255)                                       gCGGAAGCCATCCATATGGCGTCGCTGCATCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAAtt                                                                                                       >  1:462046/1‑149 (MQ=255)                                                          cGTCGCTGCATCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGttt                                                                                    <  1:180366/149‑1 (MQ=255)                                                           gTCGCTGCATCCGGCGCGAATGCTTGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTg                                                                                   >  1:299304/1‑149 (MQ=255)                                                           gTCGCTGCATCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTg                                                                                   >  2:424107/1‑149 (MQ=255)                                                             cGCTGCATCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCt                                                                                 <  2:272001/149‑1 (MQ=255)                                                                 gCATCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCtt                                                                             <  1:124146/149‑1 (MQ=255)                                                                   aTCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCAGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTa                                                                           >  2:18769/1‑149 (MQ=255)                                                                       ggCGCGAATGCTGGGTGTTGATGGTGTTCTGCGATCGCCTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTgg                                                                       <  1:118370/149‑1 (MQ=255)                                                                       ggCGCGAAGGCTGGGTGTTGATGGTGGTCTGGGGTCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGCTAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTgg                                                                       <  2:340565/149‑1 (MQ=255)                                                                         aaaacgaagctaattgaccctgaatccagatttgttgcacatgtagcccgctatCCAGCGTCGTTGCGCTGGATa                                                                                                                                               <  2:347351‑M1/21‑1 (MQ=255)                                                                         aaaacgaagctaattgaccctgaatccagatttgttgcacatgtagcccgctatCCAGCGTCGTTGCGCTGGATa                                                                                                                                               >  1:347351‑M1/55‑75 (MQ=255)                                                                               tGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAAAAAATCTGGATTCAGGGTCCATTAGCTTCGTTTTGATAGTTTGCCCCTTTATTGGGCTTTCAc                                                               <  2:392475/149‑1 (MQ=255)                                                                                  tGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGacttcacttc                                                            >  2:298081/1‑149 (MQ=255)                                                                                       gtTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCCATTCGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTccgccg                                                       >  2:39620/1‑149 (MQ=255)                                                                                        ttGATGGGGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGAAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGATCCTTTATTGGGCCTTCACTTCCCGCGt                                                      >  2:9041/1‑149 (MQ=255)                                                                                          gATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTaa                                                    >  2:95743/1‑149 (MQ=255)                                                                                          gATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTGTGCTCCTTTGTTGGGCCTTCACTTCCCCCGtca                                                    >  2:395390/1‑147 (MQ=255)                                                                                           aTGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAAGTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAg                                                   <  1:424107/149‑1 (MQ=255)                                                                                            tGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAgg                                                  <  2:462046/149‑1 (MQ=255)                                                                                                       gATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCtttcttttt                                       >  1:187231/1‑149 (MQ=255)                                                                                                         tCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCGGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCtttctttttct                                     <  2:199393/149‑1 (MQ=255)                                                                                                               aaaCCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGtt                               <  2:144866/149‑1 (MQ=255)                                                                                                                aaCCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGttt                              <  2:420102/149‑1 (MQ=255)                                                                                                                      gcgaaCGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTTCCCCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATCt                        <  2:100969/146‑1 (MQ=255)                                                                                                                       cccgctatccagcgcaacgacgctggATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGCTTTGGTctc                       >  2:260182‑M2/27‑148 (MQ=255)                                                                                                                        aaaCGCGCTAGCGTCGTTGCGCTGGATAGCTGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGTTAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATCtgt                      <  1:349490/149‑1 (MQ=255)                                                                                                                        aaaCGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATCtgt                      <  2:306498/149‑1 (MQ=255)                                                                                                                           cgcgCCAGCGTCGTTGCGCTGGATAGCGGGCCACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATCTGTGCa                   <  2:254642/149‑1 (MQ=255)                                                                                                                            tatccagcgcaacgacgctggATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGtttt                                                                                            <  2:347351‑M2/54‑1 (MQ=255)                                                                                                                            tatccagcgcaacgacgctggATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGtttt                                                                                            >  1:347351‑M2/22‑75 (MQ=255)                                                                                                                            gcgcCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCCGGATTCAGGGTCCATTAGCTTCGTTTTGAGAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATCTGTGCAg                  <  1:39620/149‑1 (MQ=255)                                                                                                                              gcCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATCTGTGCAGCg                <  2:254861/149‑1 (MQ=255)                                                                                                                                CAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTATTTCGTTTTGATCTGTGCAGCGgt              <  2:470360‑M1/149‑1 (MQ=255)                                                                                                                                    GTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATCTGTGCAGCGGTGTCg          >  1:24890‑M1/1‑149 (MQ=255)                                                                                                                                           cgctggATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATCTGTGCAGCGGTGTCGGATGCGa   <  1:18769‑M2/143‑1 (MQ=255)                                                                                                                                            gctggATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATCTGTGCAGCGGTGTCGGATGCGAc  <  2:299304‑M2/144‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                CAGTGCGCAATATGGTCGAGTTGACGGGCGTAACGCCTGCGGAAGCCATCCATATGGCGTCGCTGCATCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATCTGTGCAGCGGTGTCGGATGCGAC  >  CP009273/3274785‑3275072

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.