Read alignment evidence...
  seq id position change freq score reads annotation genes product
*NC_0009131,633,3590C→A100.0% 0.9 2intergenic (+54/‑263)ydfK/pinQcold shock protein, function unknown, Qin prophage/Qin prophage; putative site‑specific recombinase
Rejected: E-value exceeds prediction threshold.
Reads supporting (aligned to +/- strand):  new base (1/0):  ref base (1/0):  total (2/0)

ATCAATACCAGAACATTGCTTGATTACATTGAAGGAAACATAAAGAAAAAATCATGGCTGGATAACAAAGAATTATTACAAACAGCGATATCAGTTCTTAAAGACAACCAAAATTTAAATGGTAAAATGTAATATAATAAACTTACTTTTTTATCATTTTTCCACTTTAACAACATTTTGCTCCACTTTTCCACGACCAAACAACTTGAAATCTGGTTAAAATAACACGCAACACTATTCTTCTTCCTTGAGTCCGCCCGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTTCACAAAATCGATTTTGGGTCTCACCAAAATTACGGGGTTGCATACGCATTCGTTTATTTTCGAACGTGTACATACAAATATGCACAAAAATAATCATAATTATTTTCTGAGATGCATTATGATATGAACACCAATTTCGTATAGAG  >  NC_000913/1633174‑1633614
                                                                                                                                                                                         |                                                                                                                                                                                                                                                               
gtCAATACCAGAACATTGCTTGGTTAACTTGAAGAAAACATAAAGAAAAAATAATGGCTAGATAACAAAGCGGTATTACAAACAGCTATATCAGTTCTTAAAGTCAACAAAAATTTAAATGGTAAAATGTAATATAATAAACTTACTTTTTTATCATTTTTCCACTTTAACAACATTTTCAACCCATTTTCCACGCACAAACAACTTGAAAGCTGGTTAAATTAACACGCAACACTATTCTTATTCATTTAGTCCGCCCGGAACTCGAAAAACAACCCGAGTTAAAGCACTTTTTAACaaa                                                                                                                                              >  1:308570/2‑301 (MQ=11)
                                                                                                                                            acttacttTTTTATCATTTTTCCACTTTAACAACATTTTGCTCCACTTTTCCACGACCAAACAACTTGAAATCTGGTTAAAATAACACGCAACACTATTCTTCTTCCTTGAGTCCGCCCGGAACTCGAACAACAAACCGAGTTAAAGCCATTTTTCACAAAATCGATTTTGGGTCTCACCAAAATTACGGGGTTGCATACGCATTCGTTTATTTTCGAACGTTTACATACAAATATGCACAAAAATAATCATAATTATTTTTTGAATTGATTTATTATCTAAAAACAAATTTAGaataaat  >  1:486573/1‑298 (MQ=1)
                                                                                                                                                                                         |                                                                                                                                                                                                                                                               
ATCAATACCAGAACATTGCTTGATTACATTGAAGGAAACATAAAGAAAAAATCATGGCTGGATAACAAAGAATTATTACAAACAGCGATATCAGTTCTTAAAGACAACCAAAATTTAAATGGTAAAATGTAATATAATAAACTTACTTTTTTATCATTTTTCCACTTTAACAACATTTTGCTCCACTTTTCCACGACCAAACAACTTGAAATCTGGTTAAAATAACACGCAACACTATTCTTCTTCCTTGAGTCCGCCCGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTTCACAAAATCGATTTTGGGTCTCACCAAAATTACGGGGTTGCATACGCATTCGTTTATTTTCGAACGTGTACATACAAATATGCACAAAAATAATCATAATTATTTTCTGAGATGCATTATGATATGAACACCAATTTCGTATAGAG  >  NC_000913/1633174‑1633614

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 16 ≤ 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.