Read alignment evidence...
  seq id position change freq score reads annotation genes product
*NC_0140341,434,5170C→G100.0% 2.5 5intergenic (‑296/‑662)RCAP_rcc01334/RCAP_rcc01335hypothetical protein/Fis family GAF modulated sigma54 specific transcriptional regulator
Rejected: E-value exceeds prediction threshold.
Reads supporting (aligned to +/- strand):  new base (2/3):  ref base (0/0):  total (2/3)

TTTGCAGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCGCCCGCGGCG.TTTGACCTGGTCGCGG..GCAGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA  >  NC_014034/1434475‑1434577
                                          |                                                               
tcgatcgTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCT.GGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATc      <  2:911031/95‑1 (MQ=2)
gtgatcgTCGCTCCCCCCGCGGGGGCGTGGATCAAAACCTATGAGGGCT.GGCGGCCGGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATc      <  2:3831383/95‑1 (MQ=2)
  ggtggTCGCGCCCCCCGCGGGGGCGTGGATCGAAACCCCCGGCGCCGCAGCGAGTGCGTCTGGA..ACAGGATGTCGCTCCCCCCGCGGGGGCGTGGATCGaa   <  2:1437358/97‑1 (MQ=2)
  gatcgTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCT.GGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGa    >  2:3990375/5‑101 (MQ=2)
   atcgTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCT.GGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGaa   <  2:4620679/98‑1 (MQ=2)
    tcgTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCTATGAGGGCT.GGCGGCCCGGTCGTGGATCCCGCCGGTCGCTCCCCCCGCGGGGGCGTGGATCGaaa  >  1:5015058/3‑101 (MQ=2)
                                          |                                                               
TTTGCAGTCGCTCCCCCCGCGGGGGCGTGGATCGAAACCGCCCGCGGCG.TTTGACCTGGTCGCGG..GCAGCTGGTCGCTCCCCCCGCGGGGGCGTGGATCGAAA  >  NC_014034/1434475‑1434577

Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 20 ≤  ATCG  < 31 ≤  ATCG  < 39 ≤  ATCG