Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC JC	CP009273	2,770,391	IS2 (+) +5 bp	20.0%	coding (156‑160/201 nt)	ypjJ →	uncharacterized protein

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	2770391 =	38 (0.660)	8 (0.130)	8/276	NT	16.9%	coding (156/201 nt)	ypjJ	uncharacterized protein
	?	CP009273	2989720 =	NA (NA)					noncoding (1331/1331 nt)	IS2	repeat region
*	?	CP009273	= 2770395	38 (0.660)	11 (0.180)	11/276	NT	21.8%	coding (160/201 nt)	ypjJ	uncharacterized protein
	?	CP009273	= 2991050	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region

TCATTTATTTCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCT  >  CP009273/2989574‑2989864                                                                                                                                                   |                                                                                                                                                 tCATTTATTTCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTgg                                                                                                                                                <  1:259621/149‑1 (MQ=255)   atttatttCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGAtt                                                                                                                                             >  1:254403/1‑150 (MQ=255)   atttatttCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGAt                                                                                                                                              <  2:669630/149‑1 (MQ=255)      tatttCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTg                                                                                                                                           <  1:595450/149‑1 (MQ=255)        tttCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGccc                                                                                                                                        >  2:693862/1‑150 (MQ=255)           ccAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCta                                                                                                                                     >  2:964374/1‑150 (MQ=255)           ccAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCt                                                                                                                                      <  1:911794/149‑1 (MQ=255)           ccAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCt                                                                                                                                      <  2:641850/149‑1 (MQ=255)           ccAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCt                                                                                                                                      <  1:310683/149‑1 (MQ=255)                 gTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTc                                                                                                                               >  1:730880/1‑150 (MQ=255)                       cTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACa                                                                                                                         <  2:349663/150‑1 (MQ=255)                          ataaataaTCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCt                                                                                                                      <  2:26453/150‑1 (MQ=255)                              ataatCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTa                                                                                                                  <  2:617139/150‑1 (MQ=255)                                 atCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCa                                                                                                               <  1:940685/150‑1 (MQ=255)                                 atCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCa                                                                                                               <  1:1018306/150‑1 (MQ=255)                                    ccTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACtt                                                                                                            <  2:502761/150‑1 (MQ=255)                                     cTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTa                                                                                                           <  1:20866/150‑1 (MQ=255)                                      ttAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTaa                                                                                                          >  1:227856/1‑150 (MQ=255)                                       tAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAACGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAAc                                                                                                         >  2:457095/1‑150 (MQ=255)                                        aGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAATAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAAc                                                                                                         <  2:66570/149‑1 (MQ=255)                                        aGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTaa                                                                                                          <  2:244089/148‑1 (MQ=255)                                         gTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAAcc                                                                                                        >  1:200189/1‑149 (MQ=255)                                            cATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCAtt                                                                                                    <  1:1686/150‑1 (MQ=255)                                                aGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACaa                                                                                                <  1:201635/150‑1 (MQ=255)                                                   aaCCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGcc                                                                                             <  1:970040/150‑1 (MQ=255)                                                   aaCCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGcc                                                                                             <  2:319049/150‑1 (MQ=255)                                                            aaaaaaCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCg                                                                                     >  2:1027324/1‑149 (MQ=255)                                                            aaaaaaCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCg                                                                                     <  2:177425/149‑1 (MQ=255)                                                             aaaaaCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCa                                                                                   <  2:190450/150‑1 (MQ=255)                                                               aaaCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCg                                                                                     >  1:856491/1‑146 (MQ=255)                                                                 aCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGata                                                                               >  2:558746/1‑150 (MQ=255)                                                                             cAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGgc                                                                     <  1:863076/148‑1 (MQ=255)                                                                                  cTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGgcgagcga                                                               >  1:219121/1‑149 (MQ=255)                                                                                  cTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGAt                                                              <  1:317876/150‑1 (MQ=255)                                                                                   tttCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGAt                                                              >  2:480194/1‑149 (MQ=255)                                                                                          aTAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAgc                                                      >  1:834986/1‑150 (MQ=255)                                                                                           tAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAgcg                                                     <  1:572055/150‑1 (MQ=255)                                                                                              aaGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTccc                                                                          >  2:773826/1‑126 (MQ=255)                                                                                               aGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCg                                                                         <  1:773826/126‑1 (MQ=255)                                                                                                    cAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCg                                            >  1:565553/1‑150 (MQ=255)                                                                                                     aaCCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCg                                            >  1:724722/1‑149 (MQ=255)                                                                                                             aGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCAtt                                   >  2:937526/1‑150 (MQ=255)                                                                                                              gTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTc                                  >  1:424590/1‑150 (MQ=255)                                                                                                                aaaCAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGt                                >  2:207188/1‑150 (MQ=255)                                                                                                                 agcAGATCAATGGAAGTAAATTCCAATTGTTTCCTGGATTTGGCCCTTTATTTCCAGGCATCTGTTATCACTTACCCCATTACAAGCTCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCcgttcgtt                               <  2:946137/148‑1 (MQ=17)                                                                                                                   cAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTta                              >  1:808138/1‑149 (MQ=255)                                                                                                                    aGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTtata                            <  1:404912/150‑1 (MQ=255)                                                                                                                         aaTGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCt                       >  2:52163/1‑150 (MQ=255)                                                                                                                               aGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACg                 >  2:387762/1‑150 (MQ=255)                                                                                                                                  aaaTTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCct              >  2:567681/1‑150 (MQ=255)                                                                                                                                  aaaTTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCct              >  2:30020/1‑150 (MQ=255)                                                                                                                                    aTTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTATTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCctct            >  1:196933/1‑150 (MQ=255)                                                                                                                                        cAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGc          >  1:848722/1‑148 (MQ=37)                                                                                                                                           ttGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGt     <  2:511580/150‑1 (MQ=34)                                                                                                                                           gcaatatttGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGt     >  1:193167/8‑150 (MQ=1)                                                                                                                                           gaaattATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGt     >  1:232589/5‑150 (MQ=14)                                                                                                                                              tttATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCt  >  1:505753/1‑150 (MQ=32)                                                                                                                                                   |                                                                                                                                                 TCATTTATTTCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCT  >  CP009273/2989574‑2989864

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ 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.