Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,539,250 C→G 100% intergenic (‑349/+37) aroC ← / ← USA300HOU_RS07505 Chorismate synthase/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,539,2500CG100.0% 89.2 / ‑6.5 32intergenic (‑349/+37)aroC/USA300HOU_RS07505Chorismate synthase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base G (20/11);  minor base A (0/1);  total (20/12)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTGCATCATATAATCATTAATTAAAAATGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTCCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAAATAATTTTTGT  >  USA300TCH1516_ALE/1539115‑1539385
                                                                                                                                       |                                                                                                                                       
ttGCATCATATGCTCGTTATTTAACAGTGATTAGCCGTTTTGATATTCTCGTTGCGCAACTTTATCAAATGGTATACTTACTGCATTTCTTTGTATAAAGGAATGAACTGTTAATTATTAATAAAGTTAATCAGTGAGttt                                                                                                                                    <  2:577070/141‑1 (MQ=255)
ttGCATCATATAATCATTAATTAAAAATGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGttt                                                                                                                                    <  2:691408/141‑1 (MQ=255)
    atcatATAATCATTAATTAAAAATGATTAGACGTTTTAATATAATCGTATCGCAACTTTAGCAAAGAATATACTGACTACATTTCTTAATACAAAGGAACGAACTGTTAATTATTAATAAAGTTAATAAATGCGTTGaaaa                                                                                                                                >  2:295826/1‑141 (MQ=255)
     tcatATAATCATTAATTAAAAATGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATCAATAAAGGTAATCAGTGAGTATaaaaa                                                                                                                               >  2:142476/1‑141 (MQ=255)
      catATAATCATTAATTAAAAATGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTaaaaaa                                                                                                                              <  1:458172/141‑1 (MQ=255)
                        aaaTGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAatat                                                                                                            >  1:129803/1‑141 (MQ=255)
                        aaaTGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAatat                                                                                                            >  1:156042/1‑141 (MQ=255)
                        aaaTGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAataa                                                                                                            >  2:196346/1‑140 (MQ=255)
                                          atatAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATAAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCttt                                                                                          >  2:432935/1‑141 (MQ=255)
                                              aaTCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGtt                                                                                      <  1:93371/141‑1 (MQ=255)
                                                    aTCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAGCGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATAAGTTAAGCGCTTTTGTTATACtt                                                                                >  2:554950/1‑141 (MQ=255)
                                                      cGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGACCTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTAATACTTTg                                                                              >  2:271337/1‑141 (MQ=255)
                                                      cGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTATGCGCTTTTATTATACTTTg                                                                              >  2:363679/1‑141 (MQ=255)
                                                              tAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCaaa                                                                      >  2:556683/1‑141 (MQ=255)
                                                                acAAATAATAAACTGACTACATTTATTAATACAAAAGAACGAACTGTTAATTATTAATAATGTTAATCAGAAAGAAAAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCaaaaa                                                                    <  2:276038/140‑1 (MQ=255)
                                                                 aaaaTAACATACTTACTACATTTCTTAATACAAAAGAACGAACTCTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAat                                                                   <  2:272299/140‑1 (MQ=255)
                                                                     taataTACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATaa                                                               >  1:548072/1‑141 (MQ=255)
                                                                                 tACATTGCTTAATACAAAAGTACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGCTTAAAAAAATTATTATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTa                                                   <  2:418559/141‑1 (MQ=255)
                                                                                 tACAATTATTAATACGAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCATTTAAAAAAATTATGATATGAAAATATACATATGTTAAGCTCTTTTGTTATACTTTGACTTCAAAAATATATTCAATTCTTTTa                                                   <  2:225182/141‑1 (MQ=255)
                                                                                     tttCTTAATACAAAAGAACGAACTGCTAATTATTAATAAAGTTAATCAGTGCGGTTAAAAAAATTATGATATTAAAAAATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAAAATAATCAATTCTTTCACTaa                                               >  2:104199/1‑141 (MQ=255)
                                                                                         ttAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACa                                           >  2:586276/1‑141 (MQ=255)
                                                                                                aaaaGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATaaaaaa                                    <  1:597535/141‑1 (MQ=255)
                                                                                                  aaGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAata                                  >  1:123476/1‑141 (MQ=255)
                                                                                                  aaGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAata                                  >  1:431036/1‑141 (MQ=255)
                                                                                                      acgaacTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATaaa                              >  1:205993/1‑141 (MQ=255)
                                                                                                        gaacTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAAta                            >  1:154780/1‑140 (MQ=255)
                                                                                                        gaacTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATAAACAAATGTTAAGCGCTTTTGTTATACTTTGACTTCAACAATAAAATCACTTCTTTTACTACTACATAATAGATATAAATg                            >  1:662275/1‑141 (MQ=255)
                                                                                                                          aaaGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATAATTTAAAATAAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAaata          <  2:156042/141‑1 (MQ=255)
                                                                                                                          aaaGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTCAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAaata          >  2:163274/1‑141 (MQ=255)
                                                                                                                              ttAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTCAGCGCTTCTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAAATAAttt      <  1:512021/141‑1 (MQ=255)
                                                                                                                                  tCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAAATAATTTTTGt  >  2:275931/1‑141 (MQ=255)
                                                                                                                                  tCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAAATAATTTTTGt  <  1:586276/141‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                       
TTGCATCATATAATCATTAATTAAAAATGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTCCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAAATAATTTTTGT  >  USA300TCH1516_ALE/1539115‑1539385

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑