Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	2,819,278	IS5 (+) +4 bp	intergenic (‑132/+100)	csrA ← / ← alaS	carbon storage regulator/alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2288919 =	NA (NA)	42 (1.110)	38/488	0.1	100%	noncoding (1195/1195 nt)	IS5	repeat region
	?	NC_000913	2819278 =	0 (0.000)					intergenic (‑132/+103)	csrA/alaS	carbon storage regulator/alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor
*	?	NC_000913	= 2290113	NA (NA)	43 (1.140)	42/488	0.1	100%	noncoding (1/1195 nt)	IS5	repeat region
	?	NC_000913	= 2819281	0 (0.000)					intergenic (‑135/+100)	csrA/alaS	carbon storage regulator/alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor

AATTTGATAACCGTCATTTAATACTGAGTATTCTGCGGCGCCATTCATTTCAATGTACTGATACCCTCCGTTAATTTCAGTATTATTACTTACACCAAATTCTTTTATATGCTGTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTCCCATAAACCAGCTGGAT‑ATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCATTTGGTCCGCCCGAAACAGGTTGGCCAGCGTGAATAACATCGCCAGTTGGTTATCGTTTTTCAGCAACCC  >  NC_000913/2288676‑2289163                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                     aaTTTGATAACCGTCATTTAATACTGAGTATTCTGCGGCGCCATTCATTTCAATGTACTGATACCCTCCGTTAATTTCAGTATTATTACTTACACCAAATTCTTTTATATGCTGTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTCCCATAAACCAGCTGGAT‑ATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTg                                                                                                                                                                                                                                               <  1:181306/251‑1 (MQ=255)      gATAACCGTCATTTAATACTGAGTATTCTGCGGCGCCATTCATTTCAATGCACTGATACCCTCCGTTAATTTCAGTATTATTACTTACACCAAATTCTTTTATATGCTGTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTCCCATAAATCCGCCGGCT‑ATCTTTTTACAGGATAAAAACACTAACTGTCCTACCATACTCAACAGATGACGCCAATGCTATGGGCGCATATaagcaaggcccgaat                                                                                                                                                                                                                                          >  1:368676/1‑244 (MQ=255)                  ttAATACTGAGTATTCTGCGGCGCCATTCATTTCAATGTACTGATACCCTCCGTTAATTTCAGTATTATTACTTACACCAAATTCTTTTATATGCTGTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTCCCCTAAACCAGCTGGAT‑ATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAAAAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGCAAt                                                                                                                                                                                                                              >  1:198322/1‑251 (MQ=255)                           aGTATTCTGCGGCGCCATTCATTTCAATGTACTGATACCCTCCGTTAATTTCAGTATTATTACTTACACCAAATTCTTTTATATGCTGTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTTCCATTAACCAGCTTGATTAT‑TTTTTCCAGGACAACACCATCAAATGTCTCACCATACTCAACAGTTGATTCCAATGCTATGGGGGAATATTAGGCAGGTGCGAATAAACGGGGAAAtttttttctg                                                                                                                                                                                                                     >  2:99570/1‑243 (MQ=255)                                     ggcgCCATTCATTTCAATGTACTGATACCCTCCGTTAATTTCAGTATTATTACTTACACCAAATTCTTTTATATGCTGTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTCCCCTAAACCAGCTGGAT‑ATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGGGAATATaagga                                                                                                                                                                                                                                                    >  1:288247/1‑210 (MQ=255)                                     ggcgCCATTCATTTCAATGTACTGATACCCTCCGTTAATTTCAGTATTATTACTTACACCAAATTCTTTTATATGCTGTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTCCCATAAACCAGCTGGAT‑ATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATaagga                                                                                                                                                                                                                                                    <  2:288247/210‑1 (MQ=255)                                                tttCAATGTACTGATACCCTCCGTTAATTTCAGTATTATTACTTACACCAAATTCTTTTATATGCTGTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTCCCATAAACCAGCTGGAT‑ATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatttcatt                                                                                                                                                                                                  <  1:171078/249‑1 (MQ=255)                                                tttCAATGTACTGATACCCTCCGTTAATTTCAGTATTATTACTTACACCAAATTCTTTTATATGCTGTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTCCCATAAAACAGCTGGAT‑ATCTTTTTTCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatttcatta                                                                                                                                                                                                 >  2:171078/1‑249 (MQ=255)                                                       gTACTGATACCCTCCGTTAATTTCAGTATTATTACTTACACCAAATTCTTTTATATGCTGTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTCCCATAAACCAGCTGGAT‑ATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATg                                                                                                                                                                                          <  2:143968/250‑1 (MQ=255)                                                        tACTGATACCCTCCGTTAATTTCAGTATTATTACTTACACCAAATTCTTTTATATGCTGTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTCCCCTAAACCAGCTGGAT‑ATCTTTTTTCATGACAAAACCCTCCACTGTCTCACCATACTTCACCGTTGATGCCCATGATATGGGTGGATTTTAAGAAGGTGAGAAAAAGCGGGGGAATTCTTCTTGGCTGGCTCTTACATTTTATTTCTTTATGtt                                                                                                                                                                                        >  2:368776/1‑251 (MQ=255)                                                                                      ttacttacACCAAATTCTTTTATATGCTGTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTCCCATAAACCCGCTGGAA‑ATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGGGAATATAAGGAAGGTGCGAATAAGCGGGGAACTTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTTAGCCGATTTTTTCTCCCGTAAATGCCtt                                                                                                                                                          >  1:263148/1‑251 (MQ=255)                                                                                         cttacACCAAATTCTTTTATATGCTGTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTCCCATAAACCCGCTTGGT‑ATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCCATGCTATGGGGGAATATAAGGAAGGTGCGAATAAGCGGGGGAATTCTTCTCGGCTGACTCAGTTATTTCATTTCTTCCTGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGa                                                                                                                                                        >  2:176669/1‑250 (MQ=37)                                                                                           tacACCAAATTCTTTTATATGCTGTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTCCCATAAACCAGCCGGGT‑ATCTTTTTTCAGGACAACACCATCAACCGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGGGAATATAAGGAAGGAGCGAATAAGCGGGGAAATTCTTCTCGGCCGACTCCGGCATTTCCTTTTTTTCTGTTTTAGCCGATTTTTTTTCCCGTAAATGCCTTGAAtt                                                                                                                                                     >  2:184535/1‑250 (MQ=255)                                                                                                   aTTCTTTTATATGCTGTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTCCCCTAAACCAGCTGGGT‑ATTTTTTTCCAGGACAACACCATCAACCGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGGGAATATAAGGAAGGTGCGAATAAGCGGGGGAATTCTTTTCGGCTGACTCAGTCATTTCCTTTCTTCATGTTTTAGCCGATTTTTTCTCCCGTAAATGCCtt                                                                                                                                                          >  2:210675/1‑238 (MQ=255)                                                                                                   aTTCTTTTATATGCTGTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTCCCATAAACCAGCTGGAT‑ATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCtt                                                                                                                                                          <  1:210675/238‑1 (MQ=255)                                                                                                   aTTCTTTTATATGCTGTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTCCCATAAACCAGCTGGAT‑ATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTGGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCAGTTCTTCATGGTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTAtt                                                                                                                                             <  1:32347/251‑1 (MQ=255)                                                                                                                  gTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTTCCATAAAACCGCTTGAT‑ATTTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCCACCGTTGATGCCCATGATATTGGAGAATATAAGGAAGGAGCGAATAAGCGGGGAAAATCTTCTCGGCTGACTCCGTCTTTTCTTTTCTTCATGTTTGAACCGATTTTTTCTCCCGTAAATGGCTTGAATCAGCCGATTTCGACCGTTTCTTCg                                                                                                                              >  2:289859/1‑251 (MQ=255)                                                                                                                         gCCAGGATTGATTTTCGTATTATTGGCGGTCCCATAAACCAGCTGGAT‑ATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGGGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCAttt                                                                                                                        >  1:55732/1‑250 (MQ=255)                                                                                                                                  gattTTCGTATTATTGGCGGTCCCATAAACCAGCTGGAT‑ATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTAt                                                                                                              <  2:17261/251‑1 (MQ=255)                                                                                                                                         gTATTATTGGCGGTCCCATAAACCAGCTGGAT‑ATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGGGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCCTGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGt                                                                                                       >  1:243171/1‑251 (MQ=255)                                                                                                                                                                    tGGAT‑ATCTTTTTCCAGCACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATCTCAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGCGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGAtctctc                                                                                      >  1:343002/1‑241 (MQ=255)                                                                                                                                                                    tGGAT‑AGCTTGTTCCAGGACAACACCATCAACTGTCTCACCATACGCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGAgctctc                                                                                      <  2:343002/241‑1 (MQ=255)                                                                                                                                                                            cTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCAttt                                                                     >  1:93793/1‑251 (MQ=255)                                                                                                                                                                                      gACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCATTTGGTCCGCCCg                                                           >  1:45533/1‑251 (MQ=255)                                                                                                                                                                                         aacaCCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCATTTGGTCCGCCCGaa                                                         >  1:300390/1‑250 (MQ=255)                                                                                                                                                                                           cacCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAATTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCATTTGGTCCGCCCGAAACa                                                      <  2:235277/251‑1 (MQ=255)                                                                                                                                                                                               aTCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCATTTGGTCCGCCCGAAACAGGtt                                                  >  2:55390/1‑251 (MQ=255)                                                                                                                                                                                                  aaCTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCATTTGGTCCGCCCGAAACAGGTTGGc                                               >  1:336128/1‑251 (MQ=255)                                                                                                                                                                                                      gTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCATTTGGTCCGCCCGAAACAGGTTGGcct                                             <  2:243171/249‑2 (MQ=255)                                                                                                                                                                                                           cccATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCAGTTGGTCCGCCCGAAACAGGTTGGCCAGCGTGaa                                      <  2:19395/250‑1 (MQ=255)                                                                                                                                                                                                           aCCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCATTTGGTCCGCCCGAAACAGGTTGGCCAGCGTGa                                       >  1:81625/1‑250 (MQ=255)                                                                                                                                                                                                                                    gCTATGGGGGAATATAAGGAAGGTGCGAATAAGCGGGTAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAATGCGTTATCCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCATTTGGTCCGCCCGAAACAGGTTGGCCAGCGTGAATAACATCGCCCGTTGGTTATCGttt             >  2:271771/1‑251 (MQ=255)                                                                                                                                                                                                                                               atatAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCATTTGGTCCGCCCGAAACAGGTTGGCCAGCGTGAATAACATCGCCAGTTGGTTATCGTTTTTCAGCAAccc  >  1:58694/1‑251 (MQ=31)                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                     AATTTGATAACCGTCATTTAATACTGAGTATTCTGCGGCGCCATTCATTTCAATGTACTGATACCCTCCGTTAATTTCAGTATTATTACTTACACCAAATTCTTTTATATGCTGTTCTCCGCCAGGATTGATTTTCGTATTATTGGCGGTCCCATAAACCAGCTGGAT‑ATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCATTTGGTCCGCCCGAAACAGGTTGGCCAGCGTGAATAACATCGCCAGTTGGTTATCGTTTTTCAGCAACCC  >  NC_000913/2288676‑2289163

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