Read alignment evidence...
  seq id position change freq score reads annotation genes product
*NC_0009131,433,8730C→T100.0% 1.0 2intergenic (‑199/+118)pinR/ynaERac prophage; putative site‑specific recombinase/cold shock protein, Rac prophage
Rejected: E-value exceeds prediction threshold.
Reads supporting (aligned to +/- strand):  new base (1/0):  ref base (0/1):  total (1/1)

CGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCGTATGCAACCCCGTAATTTTGGTGAGACCCAAAATCGATTTTGTGAAAAATGGCTTTAACTCGGTTTGTTTTTCGAGTTCCGGGCGGACTCAAGGAAGAAGAATAGTGTTGCGTGTTATTTTAACCAGATTTCAAGTTGTTTGGTCGTGGAAAAGTGGAGCAAAATGTTGTTAAAGTGGAAAAATGATAAAAAAGTAAGTTTATTATATTACATTTTACCATTTAAATTTTGGTTGTCTTTAAGAACTGATATCGCTGTTTGTAATAATTCTTTGTTATCCAGCCATGATGTTTTCTTTA  >  NC_000913/1433667‑1434082
                                                                                                                                                                                                              |                                                                                                                                                                                                                 
cGAGACATATATAGACTTTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGCACACGTTCGAAAATAAACGAATGCGTATGCAACCCCGTAATTTTGGTGAGACCCAAAATCGATTTTGTGAAAAATGGCTTTAACTCGGTTTGTTTTTCGAGTTCCGGGCGGACTCAAg                                                                                                                                                                                                                <  1:158756/210‑1 (MQ=2)
cGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCGTATGCAACCGCGTAATTTTGGTGAGACCCAAAATCGATTTTGTGAAAAATGGCTTTAACTCGGTTTGTTTTTCGAGTTCCGGGCGGACTTAAg                                                                                                                                                                                                                >  1:54179/1‑210 (MQ=11)
                                                                                                                                                                                                              cAAGGAAGAAGAATAGTGTTGCGTGTTATTTTAACCAGATTTCAAGTTGTTTGGTCGTGGAAAAGTGGAGCAAAATGTTGTTAAAGTGGAAAAATGATAAAAAAGTAAGTTTATTATATTACATTTTACCATTTAAATTTTGGTTGTCTTTAAGAACTGATATCGCTGTTTGTAATAATTCTTTGTTATCCAGCCATGATGTTTTCTTTa  >  2:173991/1‑210 (MQ=31)
                                                                                                                                                                                                              |                                                                                                                                                                                                                 
CGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCGTATGCAACCCCGTAATTTTGGTGAGACCCAAAATCGATTTTGTGAAAAATGGCTTTAACTCGGTTTGTTTTTCGAGTTCCGGGCGGACTCAAGGAAGAAGAATAGTGTTGCGTGTTATTTTAACCAGATTTCAAGTTGTTTGGTCGTGGAAAAGTGGAGCAAAATGTTGTTAAAGTGGAAAAATGATAAAAAAGTAAGTTTATTATATTACATTTTACCATTTAAATTTTGGTTGTCTTTAAGAACTGATATCGCTGTTTGTAATAATTCTTTGTTATCCAGCCATGATGTTTTCTTTA  >  NC_000913/1433667‑1434082

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ 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.