Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	2,913,392	IS2 (–) +5 bp	coding (256‑260/2235 nt)	relA ←	GDP/GTP pyrophosphokinase

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2913392 =	0 (0.000)	32 (0.780)	30/490	0.4	100%	coding (260/2235 nt)	relA	GDP/GTP pyrophosphokinase
	?	NC_000913	= 2997691	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region
*	?	NC_000913	= 2913396	0 (0.000)	54 (1.320)	51/490	0.1	100%	coding (256/2235 nt)	relA	GDP/GTP pyrophosphokinase
	?	NC_000913	2996361 =	NA (NA)					noncoding (1331/1331 nt)	IS2	repeat region

TTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTATCGTGCCTTTTCATTTATTTCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGC  >  NC_000913/2996117‑2996606                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                      ttGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTATCGTGCCTTTTCATTTATTTCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGA‑AGTAAATTCCAATTGTTTATTGGAttt                                                                                                                                                                                                                                                 >  1:414487/1‑251 (MQ=255) ttGCCAATGGTAGTTGCCTTATATAGGGTAACAGCCATGAAAAACGACATGCGATGATATTGTGATAAATACCGATGCCGAGTTTGTATCGTGCCTTATCATTTATTTCCAGCGGTATAGCTGCTAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAACAGTGACAACCACTGAGTAAACAGATCAATGGA‑AGTACATTCCACTTGCTTATTGGAttt                                                                                                                                                                                                                                                 >  1:215186/1‑251 (MQ=255)          ccgttctccTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTGAGCGATGCCGGGTTTGTATCGTGCCATTTCATTTATTTCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACATATCAATGGA‑AGTAAATTCCAATTGTTTATTGGATTCGCCCCtata                                                                                                                                                                                                                                        <  2:286382/244‑1 (MQ=255)                 ccTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTATCGTGCCATTTCATTTATTTCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCtata                                                                                                                                                                                                                                        >  1:286382/1‑244 (MQ=255)                       ataGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTATCGTGCCTTTTCATTTATTTCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCt                                                                                                                                                                                                                           <  1:134246/251‑1 (MQ=255)                        taGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTATCGTGCCTTTTCATTTATTTCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGA‑AGTAAATTCCAATTGTTTCTTGGATTTGCCCCTATATTTCCAGACATCTg                                                                                                                                                                                                                          >  2:166424/1‑251 (MQ=255)                                       gAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTATCGTGCCTTTTCATTTATTTCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAAccc                                                                                                                                                                                                            <  1:318091/250‑1 (MQ=255)                                                                                              ccTTTTCATTTATTTCCAGCGGTATAGCTGATAAATAATCCCTTAGTGCATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATAGTCCCGTGGCGAGCGATAACCCAGCGCACTAt                                                                                                                                                    <  1:257808/251‑1 (MQ=255)                                                                                                 tttCATTTATTTCCAGCGGTATAGCTGATATATAATCCCTTAGTACATCAGGAACCTTATAAAAAAAACCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGAGGCGAGCGATAACCCAGCGCACTATg                                                                                                                                                   >  1:256540/1‑249 (MQ=255)                                                                                                 tttCATTTATTTCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATg                                                                                                                                                   <  1:358627/249‑1 (MQ=255)                                                                                                                                     cccTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCa                                                                                                              >  1:243565/1‑250 (MQ=255)                                                                                                                                           gTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCCATGGA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCt                                                                                                       >  1:12722/1‑251 (MQ=255)                                                                                                                                                           ataAAAGAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGA‑CGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAAccc                                                                                       >  2:365717/1‑251 (MQ=255)                                                                                                                                                            taAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGA‑ACTAAATTCCAATTGCTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCAAGCGCACTATGCGGATGCCATTCGTTATAGTGCTCGAACGCCTCTGCAGGGTTCTTTGCTGCCGTTACCCCg                                                                                      >  1:34018/1‑251 (MQ=255)                                                                                                                                                                  aaCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACCACCACCGAGTAAACAGATCAATGGA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATATGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGt                                                                                >  1:53186/1‑251 (MQ=255)                                                                                                                                                                   accctcgatCTGCAAACCTTTATCGATAAAAGTGACAACCACTGAGTAACCCGATAAATGGA‑AGTAAATCCCACTTGTTTATTGGATTTACCCCTATATTTCCAGACATCTGTTATCACTTCACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGAACACCAAGCGCACTATGCGGATGCCATTCGTTATCATGCCCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGtt                                                                               >  2:437016/9‑251 (MQ=17)                                                                                                                                                                   aCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTATCCCGTCTGGtt                                                                               <  2:243565/251‑1 (MQ=255)                                                                                                                                                                                            aTAAAAGGGACACACACTGAGTAAAAAGCTCCA‑GGACAGTAAATTCCAATTGTTTCTTGGATTTACCCATATATTTCCAGACATCTGTTATCGCTTACCCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGAAAACCCAGCGCACTATGCGGGTGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAAACCGTCTGGTTTGGGCATGATACTGATGTAGTCACg                                                      >  2:430618/1‑251 (MQ=11)                                                                                                                                                                                                   tGACAACCACTGAGTAAACAGATCAATGGA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATc                                               >  2:88744/1‑251 (MQ=255)                                                                                                                                                                                                    gACAACCACTGAGTAAACAGATCAATGGA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCACACATCTGTTATCACTTAACCCAGTACAAGCCCGCGGCCGCAGATATTCCCGTGGCTAACGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATTCTCGAACGCCTCTGCAAGGTTCTTTTCGGCCGTTAACCCGTCTGGTTTGTGCATGATACTGATGTAGTCACGCTTTATCg                                              <  1:423653/251‑1 (MQ=17)                                                                                                                                                                                                       aaCCACTGAGTAAACAGATCAATGGC‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGCTGTAGTTACGCTTTATCgctt                                           >  2:101936/1‑248 (MQ=255)                                                                                                                                                                                                       aaCCACTGAGTAAACAGATCAATGGA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGttt                                           <  2:123991/251‑1 (MQ=255)                                                                                                                                                                                                         ccACTGAGTAAACAGATCAATGGA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTc                                         >  2:136546/1‑251 (MQ=255)                                                                                                                                                                                                            cTGAGTAACAAGATCAATGGA‑AGTAAATTCCACTTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGACATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACg                                      >  2:348065/1‑251 (MQ=255)                                                                                                                                                                                                                        aTCAATGGA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCt                          >  2:341685/1‑251 (MQ=255)                                                                                                                                                                                                                              ggA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCg                    >  1:336222/1‑251 (MQ=39)                                                                                                                                                                                                                               gA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGt                   <  1:386044/251‑1 (MQ=38)                                                                                                                                                                                                                                              ttGTTTATTGGCTTTGCCCCTATACTATCACACAACTGTTATCACTTCACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACACAGCGCACTATGCGGATGCCATTCGTTATAATGCTAGAACGCCTCTGCAAGGTTCTTTGCTGACGTTAACCCGTCTGGTTTAGGCATGATCCTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTc     >  2:263905/1‑251 (MQ=11)                                                                                                                                                                                                                                                gTTTATTGGATTTGCCCCTAAATTTCCAGACATATGTTATCATGTAACCCACTACAAGCCCGTTGCCGCAGATAATCCCGTTGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCGCGAACGCCTCTGCCAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTTGGCATGATAGTTATGTAGTCACTCTTTATCGTTTTCACGAAGCTCACTGCTATTCCGTTTCTCTCCTGACTCCg   <  2:159637/251‑1 (MQ=11)                                                                                                                                                                                                                                                gTTTATTGGATTTGCACCTATATTTCCAGACATCTGTTATCACTTAAACCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGAGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCg   >  1:159637/1‑251 (MQ=14)                                                                                                                                                                                                                                                 tttATTGGATTTGCCCCTATATTTCCGGACATCTGTTATCACTTTACCCCTTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGACCGATAACCAAGCGCAATATGCGGAAAACATTCGTTATCATCCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCTTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCTCGAAGATCTCTGCAATTCCGTTACTTTCCGGCCTcagc  >  2:154759/1‑248 (MQ=11)                                                                                                                                                                                                                                                  ttATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATTCTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGc  <  2:398498/250‑1 (MQ=11)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                      TTGCCAATGGTTGTTGCCTTATATAGGGTAACAACGTTGAAAAACCACATGTGATGATATTGTGATAGTTAGCGATGCCGGGTTTGTATCGTGCCTTTTCATTTATTTCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGA‑AGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGC  >  NC_000913/2996117‑2996606

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ 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.