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

TACGCTGTCTGTTGATGCGGCAGTGCGCAATATGGTCGAGTTGACGGGCGTAACGCCTGCGGAAGCCATCCATATGGCGTCGCTGCATCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATCTGTGCAGCG  >  CP009273/3274765‑3275058                                                                                                                                                   |                                                                                                                                                    tACGCTGTCTGTTGATGCGGCAGTGCGCAATATAGTCGAGTTGACGGGCGTAACGCCTGCGGAAGCCATCCATATGGCGTCGCTGCATCCGGCGCGAATGCTGGGGGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCa                                                                                                                                                   >  1:298720/1‑149 (MQ=255)   gtcgcatccgacaccgctgcacagatcaaaacgaaagaaaaagaaaggccttacgggggaagtgaaggcccaataaaggagcaaactatcaaaacgaagctaattgaccctgaatccagatttgttgcacatgtagcccgctatCCAGc                                                                                                                                                 <  2:299304‑M1/5‑1 (MQ=255)    tcgcatccgacaccgctgcacagatcaaaacgaaagaaaaagaaaggccttacgggggaagtgaaggcccaataaaggagcaaactatcaaaacgaagctaattgaccctgaatccagatttgttgcacatgtagcccgctatCCAGcg                                                                                                                                                <  1:18769‑M1/6‑1 (MQ=255)      tgtctgtTGATGCGGCAGTGCGCAATATGGTCGAGTTGACGGGCGTAACGCCTGCGGAAGCCATCCATATGGCGTCGCTGCATCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGcgtc                                                                                                                                              >  2:360292/1‑149 (MQ=255)           gtTGATGCGGCAGTGCGCAATATGGTCGAGTTGACGGGCGTAACGCCTGCGGAAGCCATCCATATGGCGTCGCTGCATCCGGCGCGAATGCTGGGGGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGAGCCAGCGTCGTTgc                                                                                                                                         >  2:229280/1‑149 (MQ=255)              gATGCGGCAGTGCGCAATATGGTCGAGTTGACGGGCGTAACGCCTGCGGAAGCCATCCATATGGCGTCGCTGCATCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCt                                                                                                                                      >  1:199393/1‑149 (MQ=255)                     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                                                                                            <  1:383377/149‑1 (MQ=255)                                                        ccTGCGGAAGCCATCCATATGGCGTCGCTGCATCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCa                                                                                            <  1:396074/149‑1 (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)                                                                                                                                            aaaCGCGCTAGCGTCGTTGCGCTGGATAGCTGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGTTAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATCtgt        <  1:349490/149‑1 (MQ=255)                                                                                                                                            aaaCGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATCtgt        <  2:306498/149‑1 (MQ=255)                                                                                                                                               cgcgCCAGCGTCGTTGCGCTGGATAGCGGGCCACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATCTGTGCa     <  2:254642/149‑1 (MQ=255)                                                                                                                                                gcgcCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCCGGATTCAGGGTCCATTAGCTTCGTTTTGAGAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATCTGTGCAg    <  1:39620/149‑1 (MQ=255)                                                                                                                                                  gcCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATCTGTGCAGCg  <  2:254861/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                    TACGCTGTCTGTTGATGCGGCAGTGCGCAATATGGTCGAGTTGACGGGCGTAACGCCTGCGGAAGCCATCCATATGGCGTCGCTGCATCCGGCGCGAATGCTGGGTGTTGATGGTGTTCTGGGATCGCTTAAACCGGGCAAACGCGCCAGCGTCGTTGCGCTGGATAGCGGGCTACATGTGCAACAAATCTGGATTCAGGGTCAATTAGCTTCGTTTTGATAGTTTGCTCCTTTATTGGGCCTTCACTTCCCCCGTAAGGCCTTTCTTTTTCTTTCGTTTTGATCTGTGCAGCG  >  CP009273/3274765‑3275058

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.