Predicted mutation
evidence seq id position mutation freq annotation gene description
JC JC CP009273 2,400,257 IS5 (+) +4 bp 59.1% intergenic (‑137/‑780) lrhA ← / → alaA transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 2282398 =NA (NA)17 (0.860) 16/270 NT 64.7% noncoding (1195/1195 nt) IS5 repeat region
?CP009273 2400257 = 9 (0.470)intergenic (‑137/‑783) lrhA/alaA transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
* ? CP009273 = 2283592NA (NA)9 (0.450) 8/270 NT 49.2% noncoding (1/1195 nt) IS5 repeat region
?CP009273 = 2400260 9 (0.470)intergenic (‑140/‑780) lrhA/alaA transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2

ATTGATTTTCGTATTATTGGCGGTCCCATAAACCAGCTGGATATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGT  >  CP009273/2282281‑2282531
                                                                                                                     |                                                                                                                                     
attgcttTTCGTATTATTGGCGGTCCCATAAACCAGCCGGATATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTtctc                                                                                                        <  1:249101/149‑1 (MQ=255)
attgattTTCGTATTATTGGCGGTCCCATAAACCAGCTGGATATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAACATCAGGAAGGCGCGAATAAGCGGGGAAAtt                                                                                                              >  2:12840/1‑143 (MQ=255)
                              aaCCAGCTGGATATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGt                                                                          >  1:135075/1‑149 (MQ=255)
                                  aGCTGGATATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGa                                                                      <  1:333917/149‑1 (MQ=255)
                                    cTGGATATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGc                                                                    <  1:347295/149‑1 (MQ=255)
                                       gATATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATCCTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTg                                                                       <  2:21511/143‑1 (MQ=255)
                                             tttttCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAtttttt                                                           <  1:196694/149‑1 (MQ=255)
                                                         aacaCCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCg                                                     >  2:182149/1‑143 (MQ=255)
                                                                                                  aggCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAg      <  1:149886/147‑1 (MQ=255)
                                                                                                   tGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCGGCCTATTTAGACCGTTTCTTCGCCATTTAAgg     <  1:354425/149‑1 (MQ=255)
                                                                                                      tATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGt  >  1:335414/1‑149 (MQ=39)
                                                                                                                     |                                                                                                                                     
ATTGATTTTCGTATTATTGGCGGTCCCATAAACCAGCTGGATATCTTTTTCCAGGACAACACCATCAACTGTCTCACCATACTCAACAGTTGATGCCAATGCTATGGGTGAATATAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGT  >  CP009273/2282281‑2282531

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ 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.