Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	4,123,923	IS2 (–) +5 bp	coding (530‑534/1026 nt)	cytR ←	DNA‑binding transcriptional repressor CytR

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4123923 =	0 (0.000)	20 (1.420)	16/308	0.0	100%	coding (534/1026 nt)	cytR	DNA‑binding transcriptional repressor CytR
	?	NC_000913	4498181 =	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region
*	?	NC_000913	= 4123927	1 (0.070)	18 (1.280)	17/308	0.0	94.6%	coding (530/1026 nt)	cytR	DNA‑binding transcriptional repressor CytR
	?	NC_000913	= 4499511	NA (NA)					noncoding (1331/1331 nt)	IS2	repeat region

CCATCACATCGCTATGGCAGAAGACAGCAGTAGGCGGTTGTGGAAGATCAAGCAGCTGCTGCATCGCTTTGCTTCCGGCTTCGAAGGTGAAGTCGCCACGGGCGATGTATTGCGGATCAACCATAATGCCGCAGCGACGCAGCGCCTGAACATAGCCTTGCAGGCGGTAGTGACACAGCGGCATCTCTTCGGGACCGGCTATACAGCCAATCCGTTTATGCCCTTGCTCATATAAATAATTTACTGCATCAAATGCGGCGGTCAGATTGTCGATATGAACTGTAGGCAGCTCCAGCTCCGGTGCAAATTCGTTCGCCATCACCATCGGCGGCAGATTACGCTGTTCCTCAATGCTGGCATCAAACGGCAGCCTTGAACCCAGCAACAACATGCCATCAATTTGCTTGGTGATGATCAAATCGATAAAGGTTTTTTCCTGCTGATTTTGATGCGCACAGTCGCCAATCAGCACCAGATATCCGTGATTT  >  NC_000913/4123688‑4124175                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                         gagaaataactggctggctgcgacaccaggttgccgggcaacgagggagaccgtcagccccggttcaaagctctgctgaacaattgcgatcttgtcctgtgtggtacgcgggctgcgttgctccggccctaagacatcaatcatctggtctccaaggactagtctaaaaactagtattaagacgagcacttatttaagtgatattggttgtgtggagatgcagggggccagtctaATAATTTACTGCATCa                                                                                                                                                                                                                                               >  1:138538‑M1/236‑251 (MQ=255)      ataactggctggctgctacaccatgttgccgggcaacgagggagaccgtcatccccggttcaaagctctgctgaacaattgcgatcttttcctgtgtggtacgccgtctgcgtttctccggccctaatacatcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttagttaagtgatattggttgtctggagattcagggggccagtctaATAATTTACTGCATCAAATgc                                                                                                                                                                                                                                          >  1:237926‑M1/231‑251 (MQ=255)           gCTATGGCAGAAGACAGCAGTAGGCGGTTGTGGAAGATCAAGCAGCTGCTGCATCGCTTTGCTTCCGGCTTCGAAGGTGAAGTCGCCACGGGCGATGTATTGCGGATCAACCATAATGCCGCAGCGACGCAGCGCCTGAACATAGCCTTGCAGGCGGTAGTGACACAGCGGCATCTCTTCGGGACCGGCTATACAGCCAATCCGTTTATGCCCTTGCTCATATAAATAATtggatttgcccctatatttcc                                                                                                                                                                                                                                     >  1:297220‑M1/1‑230 (MQ=255)                      agaCAGCAGTAGGCGGTTGTGGAAGATCAAGCAGCTGCTGCATCGCTTTGATTCCGGCTTCGAAGGAGAAGTCGCCACGGGCGATGTATTGCGGATCAACCATAATGCAGCAGCGACGCAGCGCCTGAACATAGCCTTGCAGGCGGAAGTGACACAACGGCATCTCTTTGGGAACGGCTATACAGCCCATCCGTTTTTTCCCTTTCTCATATAAATAATtggcatttcccctatatttccagacatctggt                                                                                                                                                                                                                          >  1:314823‑M1/1‑219 (MQ=255)                                    gggcaacgagggagaccgtcatccccggttcaaagctctgctgaacaattgcgatcttttcctgtgtggtacgccgtctgcgtttctccggccctaagacatcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaATAATTTACTGCATCAAATGCGGCGGTCAGATTGTCGATATGAACTGTAgg                                                                                                                                                                                                            >  1:264662‑M1/201‑251 (MQ=255)                                          ggAAGATCAAGCAGCTGCTGCATCGCTTTGCTTCCGGCTTCGAAGGTGAAGTCGCCACGGGCGATGTATTGCGGATCAACCATAATGCCGCAGCGACGCAGCGCCTGAACATAGCCTGGCAGGCGGTAGTGACACAGCGGCATCTCTTCGGGACCGGCGATACAGCCAATCCGTTTATGCCCTTGCTCATATAAATAATtggatttgcccgtatatttccagacatctgttatcacttaacccattacaag                                                                                                                                                                                                      <  1:182057‑M1/251‑53 (MQ=255)                                                   ccgtcatccccggttcaaagctctgctgaacaattgcgatcttttcctgtgtggtacgccgtctgcgtttctccggccctaagacagcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaATAATTTACTGCATCAAATGCGGCGGACAGATTGTCGATATGAACTGTAGGCAGCTCCACCTCCgg                                                                                                                                                                                             <  1:18811‑M1/66‑1 (MQ=255)                                                       catccccggttcaaagctctgctgaacaattgcgatcttttcctgtgtggtacgccgtctgcgtttctccggccctaagacatcaatcatctgttcgccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattgggtgtctggagatgcagggggccagtctaATAATTTACTGCATCAAATGCGGCGGTCAGATTGtcn                                                                                                                                                                                                                          >  1:39942‑M1/182‑217 (MQ=255)                                                           ctgcATCGCTTTGCTTCCGGCTTCGAAGGTGAAGTCGCCACGGGCGATGTATTGCGGATCAACCATAATGCCGCAGCGCCGCAGCGCCTGAACATAGCCTTGCAGGCGGTAGTGACACAGCGGCATCTCTTCCGGACCGGCTATACAGCCAATCCGTTTATGCCCTTTCTCATATAAATAATtggtttttcccccatatttaccgacatcttttttcacttaacccattaccaccccg                                                                                                                                                                                                  >  1:244255‑M1/1‑182 (MQ=255)                                                                          tCCGGCTTCGAAGGTGAAGTCGCCACGGGCGATGTATTGCGGTTCAACCATAATGCCGCAGCGACGCAGCGCCTGAACATAGCCTTGCAGGCGGTAGTGACACAGCGGCATCGCTTCGGGACCGGCTATACAGCCAATCCGTTTATGCCCTTGCTCATATAAATAATtggatttgcccctatagttccagacatctgttatcacttaacccattacaagcccgctgccgcagatattcccgtggcgagc                                                                                                                                                                        <  1:142429‑M1/249‑83 (MQ=255)                                                                                    agagagactgcgtgtcacgttcgcgccgtctgcgtttctccggccctaagacatcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaATAATTTACTGCATCAAATGCGGCGGTCAGATTGTCGATATGAACTGTAGGCAGCTCCAGCTCCGGTGCAAATTCGTTCGCCATCACCATCGGCGGCAg                                                                                                                                                            >  1:110104‑M1/153‑251 (MQ=255)                                                                                      ncgatcttttcctgtgtggtacgccgtctgcgtttctccggccctaagacatcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaATAATTTAc                                                                                                                                                                                                                                                      <  1:191484‑M1/9‑1 (MQ=255)                                                                                           aggcgccACGTGCGATGTATTGCGGATCAACCATAATGCCGCAGCGACGCAGCGCCTGAACATAGCCGTGCAGGCGGTAGTGACACAGCGGCATCTCTTCGGAACCAGCTATACATCTAATCCGTTTATGCCCTTGCTCATATAAATAATtggatttccccttatatctccagacatctgtgaacacttaacccagttcaagcccgctgccccagatattcccttggcgagcgataacccagctcactatg                                                                                                                                                     <  1:318608‑M1/248‑102 (MQ=255)                                                                                                     gtnnnnngccntctgcgtttctccggccctaagacatcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaATAATTTAc                                                                                                                                                                                                                                                      >  2:191484‑M1/136‑144 (MQ=255)                                                                                                       ngtacgccgtctgcgtttctccggccctaagacatcaatcatctgttctagaatgactagtctaaaaactcgtatttagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaATAATTTACTGCATCAAATGCGGCGGTCAGATTGTCGATATGAACTGTAGGc                                                                                                                                                                                                           <  1:66425‑M1/52‑1 (MQ=255)                                                                                                           cgccgtctgcgtttctccggccctaagacatcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaATAATTTACTGCATCAAATGCGGCGGTCAGATTGTCGATATGAACTGTAGGCAGCTCCAGCTCCGGTGCAAATTCGTTCACCATCACCATCGGCGGCAGATTACGCTGTTCCTCAATGCTgg                                                                                                                                     >  1:45332‑M1/130‑251 (MQ=255)                                                                                                                 cGGATCAACCATAATGCCGCAGCGACGCAGCGCCTGAACATAGCCTTGCAGGCGGTAGTGACACAGCGGCATCTCTTCGGGACCGGCTATACAGCCAATCCGTTTATGCCCTTGCTCATATAAATAATtggatttgcccctatatttccagacatctgttatcacttaacccattacaagcccgctgccgccgatattcccgtggcgagcgataacccagcgcactatgcggatgccattcgttataatgc                                                                                                                               >  1:20254‑M1/1‑128 (MQ=255)                                                                                                                                     gacatcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaATAATTTACTGCATCAAATGCGGCGGTCCGATTGTCGATATGAACTGTAGGCAGCTCCAGCTCCGGTGAAAAttcg                                                                                                                                                                                   <  1:294265‑M1/76‑1 (MQ=255)                                                                                                                                      gCGACGCAGCGCCTGAACATAGCCTTGCAGGCGGTAGTGACACAGCGGCATCTCTTCGGGACCGGCTATACAGCCAATCCGTTTATGCCCTTGCTCATATAAATAATtggatttgcccctatatttccagacatctgttatcacttaacccattacaagcccgctgccgcagatattcccgtggcgagcgataacccagcgcactatgcggatgccattcgttataatgctcgaacgcctctgcaaggttc                                                                                                          <  1:120816‑M1/251‑145 (MQ=255)                                                                                                                                        atcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttgtcttgagattcagggggccagtctaATAATTTACGGCATCAAATGCGGCGGTCAGATTGTCGATATGAACTGTAGGCAGCTCCAGCTCCGGTGCAAATTCGTTCGCCATCACCATCGGCGGGATATTGCGCTGTTCCTCAATGCTGGCATCAAACGGCAGCCTTGAACCCAGcaac                                                                                                        >  1:153572‑M1/101‑251 (MQ=255)                                                                                                                                                      aCATAGCCTTGCAGGCGGTAGTGACACAGCGGCATCTCTTCGGGACCGGCTATACAGCCAATCCGTTTATGCCCTTGCTCATATAAATAATtggatttgcccctatatttccagacatctgttatcacttaacccattacaagcccgctgccgcagatattcccgtggcgagcgataacccagcgcactatgcggatgccattcgttataatgctcgaacgcctctgcaaggttctttgctgccggtaacc                                                                                          <  1:71350‑M1/251‑161 (MQ=255)                                                                                                                                                        aTAGCCTTGCATGCGGTAGTGACACAGCGGCATCGCTTCGGTAACGGCTATACAGCCAATCCGTTTATGCCCTTGCTCATATAAATAATtggatttgcccctatatttccagacatctgttatcacttaacccattacaagcccgctgccgcagatattcccgtggcgagcgataacccagcgcactatgcggatgccattcgttataatgctcgaacgcctctgcaaggttctttgctgccgttaacccg                                                                                        <  1:6676‑M1/251‑163 (MQ=255)                                                                                                                                                                  gtctaaaaactagtattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaATAATTTACTGCATCAAATGCGGCGGTCAGATTGTCGATATGAACTGTAGGCAGCTCCAGCTCCGGTGCAAATTCGTTCGCCATCACCATCGGCGGCAGATTACGCTGTTc                                                                                                                                                >  1:284782‑M1/75‑185 (MQ=255)                                                                                                                                                                      ggTAGTGACACAGCGGCATCTCTTCGGGACCGGCTATACAGCCAATCCGTTTATGCCCTTGCTCATATAAATACTtggatttgcccctatatttccagacatctgttatcacttaacccattacaagcccgctgccgcagatattcccgtggcgagcgataacccagcgcactatgcggatgccattcgttataatgctcgaacgcctctgcaaggttctttgctgccgttaacccgtctggtttgggcat                                                                          >  1:170741‑M1/1‑75 (MQ=255)                                                                                                                                                                            gACACAGCGGCATCTCTTCGGGACCGGCTATACAGCCAATCCGTTTATGCCCTTGCTCATATAAATAATtggatttgcccctatatttccagacatctgttatcacttaacccattacaagcccgctgccgcagatattcccgtggcgcgcgataacccagcgcactatgcggatgccattcgtt                                                                                                                                      >  1:172654‑M1/1‑69 (MQ=255)                                                                                                                                                                               tattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaATAATTTACTGCATCAAATGCGGCGGTCAGATTGTCGATATGAACTGTAGGCAGCTCCAGCTCCGGTGCAAATTCGTTCGCCATCACCATCGGCGGCAGATTACGCTGTTCCTCAATGCTGGCATCAAACg                                                                                                                            >  1:138995‑M1/62‑192 (MQ=255)                                                                                                                                                                                               tatttaagtgatattggttgtctggagattcagggggccagtctaATAATTTACTGCATCAAATGCGGCGGTCAGATTGTCGATATGAACTGTAGGCAGCTCCAGCTCCGGTGCAAATTCGTTCGCCATCACCATCGGCGGCAGATTACGCTGTTCCTCAATGCTGGCATCAAACGGCAGCCTTGAACCCAGCAACAACATGCCATCAATTTGCTTGGTGATGATCAAATCGATAAAGGTTTTTTCcng                                                   >  1:255900‑M1/46‑249 (MQ=255)                                                                                                                                                                                                   ccGGCTATACAGCCAATCCGTTTATGCCCTTGCTCATATAAATAATtggatttgcccctatatttccagacatctgttatcacttaacccattacaagcccgctgccgcagatattcccgtggcgagcgataacccagcgcactatgcggatgccattcgttataaggctcgaacgcctctgcaaggttctttgctgccgttaacccgtcttgtttgggcatgatactgatgtagtcacgctttatcgttt                                             <  1:321011‑M1/251‑206 (MQ=255)                                                                                                                                                                                                     ngcTATACAGCCAATCCGTTTATGCCCTTGCTCATATAAATAATtggatttgcccctatatttccagacatctgttatcacttaacccattacaagcccgctgccgcagatattcccgtggcgagcgttaacccagcgcactatgcggatgccattcgttataatgctcgaacgcctctgcaaggttctttgctgccgttaacccgtctggtttgggcatgatactgatgtagtcacgctttatcgttttc                                           >  1:81078‑M1/2‑44 (MQ=255)                                                                                                                                                                                                              ggttgtctggagattcagggggccagtctaATAATTTACTGCATCAAATGCGGCGGTCAGATTGTCGATATGAACTGTAGGCAGCTCCAGCTCCGGTGCAAATTCGTTCGCCATCACCATCGGCGGCAGATTACGCTGTTCCTCAATGCTGGCATCAAACGGCAGCCTTGAACCCAGCAACAACATGCCATCAATTTGCTTGGTGATGATCAAATCGATAAAGGTTTTTTCCTGCTGATTTTGATGCGca                                   >  1:5624‑M1/31‑250 (MQ=255)                                                                                                                                                                                                              gCCAATCCGTTTATGCCCTTGCTCATATAAATAATtggatttgcccctctatttccacacatctgttatcacttaacccattacaagcccgctgccgcagatattcccgtggcgcgcgataacccagcgcactatgcggatgccattcgttataatgctcgaac                                                                                                                         >  1:147370‑M1/1‑35 (MQ=255)                                                                                                                                                                                                                 aaTCCGTTTATGCCCTTGCTCATATAAATAATtggatttgcccctatatttccagacatctgttatcacttaacccattacaagcccgctgccgcagatattcccgtggcgagcgataacccagcgcactatgcggatgccattcgttataatgctcgaacgcctctgcaaggttctttgctgccgttaacccgtctggtttggg                                                                             <  1:150052‑M1/205‑174 (MQ=255)                                                                                                                                                                                                                   tctggagattcagggggccagtctaATAATTTACTGCATCAAATGCGGCGGTCAGATTGTCGATATGAACTGTAGGcagc                                                                                                                                                                                                        >  1:71896‑M1/26‑80 (MQ=255)                                                                                                                                                                                                                            gCCCTTGCTCATATAAATAATtggatttgcccctatatttccagacatctgttatcacttaacccattacaagcccgctgccgcagatattcccgtggcgagcgataacccagcgcactatgcggatgtcattcgttataatgctcgaacgcctttgcaagtgtcgttgctgccgttaacccgtcgggtttgggcatgatcctgatgtagtcacgctttatcgttttcacgaagctctctgctattccgt                     <  1:189991‑M1/250‑230 (MQ=255)                                                                                                                                                                                                                             cagggggccagtctaATAATTTACTGCATCAAATGCGGCGGTCAGATTGTCGATATGAACTGTAGGCAGCTCCAGCTCCGGTGCAAATTCGTTCGCCATCACCATCGGCGGCAGATTACGCTGTTCCTCAATGCTGGCATCAAACGGCAGCCTTGAACCCAGCAACAACATGCCATCAATTTGCTTGGTGATGATCAAATCGATAAAGGTTTTTTCCTGCTGATTTTGATGCGCACAGTCGCCCATCAGc                    <  1:14648‑M1/235‑1 (MQ=255)                                                                                                                                                                                                                              agggggccagtctaATAATTTACTGCATCAAATGCGGCGGTCAGATTGTCGATGTGAACTGTAGGCAGCTCCAGCTCCGGTGCAAATTCGTTCGCCATCACCATc                                                                                                                                                                    >  1:97646‑M1/15‑105 (MQ=255)                                                                                                                                                                                                                               gggggccagtctaATAATTTACTGCATCAAATGCGGCGGTCAGATTGTCGATATGAACTGTAGGCAGCTCCAGCTCCGGTGCAAATTCGTTCGCCATCACCATCGGCGGCAGATTACGCTGTTCCCCAAt                                                                                                                                          >  1:149966‑M1/14‑130 (MQ=255)                                                                                                                                                                                                                                     cATATAAATAATtggatttgcccctatatttccagacatctgttatcacttaacccattacaagcccgctgccgcagatattcccgtggcgagcgataacccagcgccctatgcggatgccattcgttataatgctcgaacgcctctgtcaggttctttgctgccgttaac                                                                                           >  1:321314‑M1/1‑12 (MQ=255)                                                                                                                                                                                                                                           aataatTTACTGCATCAAATGCGGCGGTCAGATTGTCGATATGAACTGTAgg                                                                                                                                                                                                            <  1:263334/52‑1 (MQ=255)                                                                                                                                                                                                                                              aatTGACTTCATCAAATGCGGCGGTCAGATTGTCGATATGAACTGTAGGCAGCTCCAGCTCCGGTGCAAATTCGTTCGCCATCACCATCGGCGGCAGATTACGCTGTTCCTCAATGCTGGCATCAATCGGCAGCCTTGAACCCAGCAACAACATGCCATCAATTTGCTTGTTGAGGAGCAAATCGATAAAGGGTTTTTCCTGCTGATTTTGATGCGCACAGTCGCCAATCAGCACCAGATATCCGTGAttt  <  1:297296/251‑1 (MQ=255)                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                         CCATCACATCGCTATGGCAGAAGACAGCAGTAGGCGGTTGTGGAAGATCAAGCAGCTGCTGCATCGCTTTGCTTCCGGCTTCGAAGGTGAAGTCGCCACGGGCGATGTATTGCGGATCAACCATAATGCCGCAGCGACGCAGCGCCTGAACATAGCCTTGCAGGCGGTAGTGACACAGCGGCATCTCTTCGGGACCGGCTATACAGCCAATCCGTTTATGCCCTTGCTCATATAAATAATTTACTGCATCAAATGCGGCGGTCAGATTGTCGATATGAACTGTAGGCAGCTCCAGCTCCGGTGCAAATTCGTTCGCCATCACCATCGGCGGCAGATTACGCTGTTCCTCAATGCTGGCATCAAACGGCAGCCTTGAACCCAGCAACAACATGCCATCAATTTGCTTGGTGATGATCAAATCGATAAAGGTTTTTTCCTGCTGATTTTGATGCGCACAGTCGCCAATCAGCACCAGATATCCGTGATTT  >  NC_000913/4123688‑4124175

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ 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.