Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,947,803	G→A	I55I (ATC→ATT)	hdfR ←	DNA‑binding transcriptional dual regulator HdfR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,947,803	0	G	A	81.8%	12.5 / ‑0.0	11	I55I (ATC→ATT)	hdfR	DNA‑binding transcriptional dual regulator HdfR
Reads supporting (aligned to +/- strand):  ref base G (1/1);  new base A (7/2);  total (8/3)
Fisher's exact test for biased strand distribution p-value = 4.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.95e-01

CTTCGAACTGTAAGCCTGTATGGGCATCCTGATTTTGATACAAGCGTCCCAGCCACTGATTAAGCATACATTCCCACAACGAGGCGCTGGCACCGATAGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAA‑GGTTCACACCCAGTTGATTTTCCAGTTG‑TCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACC‑AAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATGATTTAAATGTTTTGTTTTACACTCTG  >  NC_000913/3947595‑3948024                                                                                                                                                                                                                 |                                                                                                                                                                                                                                 cTTCGAACTGTAAGCCTGTATGGGCATCCTGATTTTGATACAAGCGTCCCAGCCACTGATTAAGCATACATTGCCACAACGAGGCGCTGGCACCGATAGAAAAATCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGAATATTGTTTCTGTGGCggggggaaaagtttcaacccaaatcg                                                                                                                                                                                        >  1:270125/1‑228 (MQ=255)       aCTGTAAGCCTGTATGGGCATCCTGATTTTGATACAAGCGTCCCAGCCACTGATTAAGCCTACATTCCCACACCGAGGCGCTGGCACCGATAGAAACCTCGTTATGTAGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGAATATTGTTTCTGTGGCGGGTGAAAA‑AGTTTACACCCAGTTGAtttgat                                                                                                                                                                                 >  1:210309/1‑248 (MQ=255)                                                             tAAGCATACATTCCCACAACGAGGCGCTGGCACCGATAGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGAATATTGTTTCTGTGGCGGGTGAAAA‑GGTTCACACCCAGTTGATTTTCCAGTTG‑TCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGc                                                                                                                           <  1:93699/250‑1 (MQ=255)                                                                                                                   gTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGAATATTGTTTCTGTGGCGGGTGAAAA‑GGTTCACACCCAGTTTATTTTCCAGTTG‑TCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACC‑AAAGTGACGCGTTCGGc                                                                                                <  1:227298/222‑1 (MQ=255)                                                                                                                        gTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCt                                                                                                                                                                                                                       >  1:188149/1‑101 (MQ=255)                                                                                                                              nccACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAACGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGAATATTGTTTCTGTGGCGGGCGAAAA‑GGGTCACACCCCGCTGGTTTTTCCGCTT‑TCTGATTCGAAAGCTCACTGCTGGCTGGGTCCGATAGAGCGGTTTAGCCGCTCGACC‑AAAAAGACGCGTTCGGCTAACTTTCTGGACAGATTTTAACAATTACGTATCcac                                                           >  1:60977/2‑248 (MQ=255)                                                                                                                                cACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAA‑GGTTCACACCCAGTTGATTTTCCAGTTG‑TCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACC‑AAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGc                                                      <  1:120985/251‑1 (MQ=255)                                                                                                                                   ctcctTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGAATATTGTTTCTGTGGCGGGTGAAAA‑AGTTCACCCCCAGCTGATTTTccc                                                                                                                                                                                >  1:178184/1‑127 (MQ=255)                                                                                                                                                nccTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGAATATTGTTTCTGTGGCGGGGGAAAAAGGTT‑ACACCCAGTTGATTTTCCAGTTG‑TCTTGTTCTAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCCCCCGACC‑AAAGTGACGCGGTCGGCTAACTTCCAGGAAAGTTTTTTACAATTCCGTATCCACCATGCTCTCCGccgatcgga                                       >  1:65894/2‑242 (MQ=255)                                                                                                                                                  ntGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGAATATTGTTTCTGTGGCGGGTGGAAA‑GGTGCACACCCCGGTGTTTTTTCAGTTGGTTTG‑TTTGAAAGCTCACTGCTGGATGGGGGCGATAGAGCGATTCAGCCGCTCGACCCAAAG‑GACGCGGTCGGCTAACTTCCAGGGAAGTTTTTAACAATTTCGTATCCCCAGTGCTCTCCGCCAAATTATTTg                                    >  1:60279/2‑251 (MQ=255)                                                                                                                                                                                    agtagtTTTTCACAGGCAGCGGTTAAACGAATATTGTTTCTGTGGCGGGTGAAAA‑AGTTCAAACCCAGGTGATTTTCCAGTTG‑GTTTATTTGAAAGTTCACTGCTGACTGGGGCAGATAGAGGGATTTAGCCGCTCGGCC‑AAAGTGAAGCGTTCGGCTAACTTCCAGGAAAGATTTTTACAATTTCGTATCAACAGTGCGCTCCCCAAAATTATTTTTCGTTATGAGTTAAATTTTTTGTTTTACActctt  >  1:12956/1‑250 (MQ=255)                                                                                                                                                                                                                 |                                                                                                                                                                                                                                 CTTCGAACTGTAAGCCTGTATGGGCATCCTGATTTTGATACAAGCGTCCCAGCCACTGATTAAGCATACATTCCCACAACGAGGCGCTGGCACCGATAGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAA‑GGTTCACACCCAGTTGATTTTCCAGTTG‑TCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACC‑AAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATGATTTAAATGTTTTGTTTTACACTCTG  >  NC_000913/3947595‑3948024

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑