Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	3,078,723	IS5 (+) +4 bp	coding (134‑137/1389 nt)	cmtA ←	mannitol‑specific PTS enzyme IICB component CmtA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	3078723 =	1 (0.020)	34 (0.600)	32/490	0.7	97.1%	coding (137/1389 nt)	cmtA	mannitol‑specific PTS enzyme IICB component CmtA
	?	NC_000913	= 3131340	NA (NA)					noncoding (1195/1195 nt)	IS5	repeat region
*	?	NC_000913	= 3078726	1 (0.020)	49 (0.860)	47/488	0.3	98.0%	coding (134/1389 nt)	cmtA	mannitol‑specific PTS enzyme IICB component CmtA
	?	NC_000913	3130146 =	NA (NA)					noncoding (1/1195 nt)	IS5	repeat region

GTTGCTGAAAAACGATAACCAACTGGCGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATCACCTCTGGGTAAAAACTTTTACCCAGCAAACCCGCTGGCGTTCCGGCGGCGTCGAAGAAT  >  NC_000913/3131098‑3131569                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                         gTTGCTGAAAAACGATAACCAACTGGCGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCa                                                                                                                                                                                                                                  <  1:539099/251‑1 (MQ=11)       gAAAAACGAGAACGAACGTGCGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAAGGATACGTCAGTGGGAGAGACCTCAATATAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCGAAATAGGCTGATGCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGACATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTGCCCTAAATCAGGTc                                                                                                                                                                                                                              <  2:307245/249‑1 (MQ=11)                      aCTGGCGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACt                                                                                                                                                                                                             <  1:315825/251‑1 (MQ=40)                                   ttCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAacac                                                                                                                                                                                               >  1:562215/1‑251 (MQ=255)                                           ggCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCCCCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGaa                                                                                                                                                                                       >  2:496789/1‑250 (MQ=255)                                              cAACCTGTTGCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGa                                                                                                                                                                                   <  2:19595/251‑1 (MQ=255)                                                      ttCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCtt                                                                                                                                                                            <  2:562215/250‑1 (MQ=255)                                                              gACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGAATGAGTCAGCCGAGAAGAATTACCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGAt                                                                                                                                                                  >  2:515633/1‑251 (MQ=255)                                                                               gTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGCTTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGACTTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACACCGCGAGCGcc                                                                                                                                                  >  1:37929/1‑250 (MQ=255)                                                                               gTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGGGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACACCGCGGGCGccc                                                                                                                                                 >  1:334645/1‑250 (MQ=255)                                                                                tGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACACCGCGAGCGccac                                                                                                                                                >  2:7722/1‑251 (MQ=255)                                                                                   gagagaTCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACACCGCGAGCGccacc                                                                                                                                               >  2:214723/1‑249 (MQ=255)                                                                                              cTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACACCGCGCACGCCACCAGCATACCGATTc                                                                                                                                  >  2:485401/1‑251 (MQ=255)                                                                                                aaaaaCTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAATAAATGAAATGACTGAGTCAGCTGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGAGACTTATC‑GCCAAATACC‑AGTGAAAAGAGCGGTTCCCCCGA‑GATCTACACCGCGAGCGCCACCAGAATACCGATTc                                                                                                                                  <  2:536057/249‑1 (MQ=17)                                                                                                  aaaCTGGGGATAACGCCTTGAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAACCACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACACCGCGAGCGCCACCAGAATACCGATTccgcc                                                                                                                              >  1:294620/1‑251 (MQ=255)                                                                                                    aCTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACACCGCGAGCGCCACCAGAATACCGATTccgcccc                                                                                                                            >  1:574985/1‑250 (MQ=255)                                                                                                       ggggATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATg                                                                                                                                                                                    >  1:10351/1‑193 (MQ=255)                                                                                                       ggggATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATg                                                                                                                                                                                    <  2:10351/193‑1 (MQ=255)                                                                                                                 ccTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCgg                                                                                                                >  1:420010/1‑250 (MQ=255)                                                                                                                    tAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACtt                                                                                                            >  1:293268/1‑251 (MQ=255)                                                                                                                       aTGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACAGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTcac                                                                                                         >  1:251435/1‑251 (MQ=255)                                                                                                                                aaaCGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAGATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACACAGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGGAAACCGGACTTCACACCTacccc                                                                                                >  2:498081/1‑247 (MQ=255)                                                                                                                                 aaCGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAACTCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAaca                                                                                                                                                                                                >  1:363222/1‑156 (MQ=255)                                                                                                                                 aaCGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAAGCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAaca                                                                                                                                                                                                <  2:363222/156‑1 (MQ=255)                                                                                                                                      tCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACgg                                                                                          >  1:203050/1‑251 (MQ=255)                                                                                                                                              ggCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACACCCCCGGTCtggtgg                                                                                  >  2:497794/1‑251 (MQ=255)                                                                                                                                                    ttCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAg                                                                                                                                                                                                                                 <  1:498501/105‑1 (MQ=32)                                                                                                                                                    ttCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAg                                                                                                                                                                                                                                 >  2:498501/1‑105 (MQ=32)                                                                                                                                                        aGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATc                                                                        >  1:26204/1‑251 (MQ=255)                                                                                                                                                           aattacggggAAAAAAAATCGG‑TCAAAACATGAAGAAATAAATTGATTGAGTCAGCAGAGAAGAATTCCCCCGTTTCTTCCCACCTCCCCTAAACCAGCTCATCCGCTTCGAAAT‑CTTAACCACCAAAACCC‑GGCGAAAGGCGGGGCTGGCC‑GCCGAACACCACCGCGAGCCCCACCATAATCCCGAGTCCCCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTaa                                                                     <  1:254854/244‑1 (MQ=255)                                                                                                                                                            atttgagggAGAAAAAATCGGCTCAAA‑CATGAAGAAATGGAATGACTGAGTCAGCAGAGAAGAATTTCCCCGCTTATTCGCAACTTACCTAAATCAGGACATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACAACGCGCGCGCCAACAGAATACCGATTCCTCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTACCGCGCGGATCTaa                                                                     >  2:259199/7‑250 (MQ=37)                                                                                                                                                                                                       ggatggAGTCAGCCGAAAAGAAGCCCCCCGCTTATCCCCCCCTTCCCTAAACCAGTACATACGCTGCGATATCCTTACC‑GCAAAACACC‑AGAAAAAGGGGCGGCTTGCC‑GACGACCAACCCCGGGCGCCCCACAAAAACACCTATCCCCCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATCACCTCTGGGTAAAAACTTTTACCCAGCAAACCCGCt                          <  1:331848/246‑1 (MQ=255)                                                                                                                                                                                                            gAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATCACCTCTGGGTAAAAACTTTTCCCCAGCAAACCCGCTGGCGt                     >  2:9145/1‑251 (MQ=255)                                                                                                                                                                                                                         aaaactcccccgttttttccccccctCCCTAAATTAGGTCATCCGCTGCGAGATACT‑AAC‑CCCAAACCCCCAGAAAAATGGGCGGCTTCCC‑GACGTCCACCCCCGCGCCCCCCACCAGAATACCGTCCCCCCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATCACCTCTGGGTAAAAACTTTTACCCAGCAAACCCGCTGGCGTTCCGGCGGCGTCg        <  1:356661/226‑1 (MQ=255)                                                                                                                                                                                                                               tCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATCACCTCTGGGTAAAAACTTTTACCCAGCAAACCCGCTGGCGTTCCGGCGGCGTCGAAGAAt  >  1:93851/1‑251 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                         GTTGCTGAAAAACGATAACCAACTGGCGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAA‑CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAAC‑GCCAAACACC‑AGCGAAATGAGCGGCTTGCC‑GACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATCACCTCTGGGTAAAAACTTTTACCCAGCAAACCCGCTGGCGTTCCGGCGGCGTCGAAGAAT  >  NC_000913/3131098‑3131569

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ 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.