Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,824,443	G→A	A682T (GCG→ACG)	spoT →	bifunctional (p)ppGpp synthase/hydrolase SpoT

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,824,443	0	G	A	87.5%	37.3 / ‑5.3	16	A682T (GCG→ACG)	spoT	bifunctional (p)ppGpp synthase/hydrolase SpoT
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (5/9);  minor base C (2/0);  total (7/9)
Fisher's exact test for biased strand distribution p-value = 1.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGAAGTTTATGGCTGTGGAATGGGATAAAGAGACGGCGCAGGAGTTCATCACCGAAATCAAGGTGGAGATGTTCAATCATCAGGGTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTAATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTCGTACCGCAGATGCCGTTGGCGTACATGAAGTTCACGCC  >  NC_000913/3824228‑3824664                                                                                                                                                                                                                        |                                                                                                                                                                                                                              agaAGTTTATGGCTGTGGAATGGGATAAAGAGACGGCGCAGGAGTTCATCACCGAAATCAAGGTGGAGATGTTCAATCATCAGGGTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGACGAATATCATGCGCAAAATCCGCGTGATGCCAGAc                                                                                                                                                                                            <  1:259076/251‑1 (MQ=255)               gtgGAAGGGGATAAAGAGACGGCGCAGGAGTTCATCACCGAAATCAAGGTGGAGATGTTCAATCATCAGGGTGCGCTGGCAAACCTGACTGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCAGCTGACGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAgn                                                                                                                                                                                 <  1:101744/248‑2 (MQ=255)                                                                            atcatcAGGGTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGACGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAAGTAATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTc                                                                                                                 <  1:414414/251‑1 (MQ=255)                                                                                       gcgcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGGTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGACGAATATCATgcg                                                                                                                                                                                                                  <  1:447931/143‑1 (MQ=255)                                                                                             gCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGACGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTAATGTTTTATGAACCCAACACGTTATgn                                                                                                                                    <  1:129250/215‑2 (MQ=255)                                                                                              cAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGGCTACGGACGAGCAAGATGGTAGCGCCTACAGCGCCTTTAGTCGTATGGCCGCTCGCGACCGCGTGCATCTGACGACTATAATGAGCACAATACGCGTGATGCCAGCCGTGATTAACGTCACCCGGAACCGAAATTAATGATTTATGAACCCACCACGTTATGCACGCCTCTGAGAAATGCtaaccagccggccgc                                                                                                    >  1:363426/1‑232 (MQ=255)                                                                                                             cAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTTGCGTCTACCACGCATTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGACGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAACTTAATGTTTTATGAACCcaccac                                                                                                                                           >  1:476857/1‑192 (MQ=255)                                                                                                                                                                          cTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGACGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTAATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTcc                                                                      <  1:420719/200‑1 (MQ=255)                                                                                                                                                                                 gcCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGCAGAATATCATGCGCACAATCCGCGTGATGCCAGACGTGATTAAAGTCACccgaaaccgaaa                                                                                                                                                                  >  1:491404/1‑101 (MQ=255)                                                                                                                                                                                   cTTTATTCGGCGGACCGCTCGTGACCGTGTGCATCTGACGAATATCATGCGCAAAAGCCGCTTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTAATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGc                                                                                                                   <  1:469180/146‑1 (MQ=255)                                                                                                                                                                                    tttATTCGTCTGACCGCTCGTGACCGTGTGCATCTGACGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTAATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGc                                                                            <  1:114275/184‑1 (MQ=255)                                                                                                                                                                                    tttATTCGTCTGACCGCTCGTGACCGNGTGCATNNGCNGAATATCATGCGCAAAATCNGCNNNANNNCNGCCGTNATNNAAGTCACCCNAAACCGAAATTAATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAANGCTCGCCAGNNGGCAGCCTGATCTGACCGTCTNCATnnannanctc                                                                       >  2:114275/1‑185 (MQ=255)                                                                                                                                                                                     ttATTCGTCTGACCGCTCGTGGCCGTGTGCAGCTGACGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTATTGGTTTATTAACCCAACACTGTATGCAGGCATCTGCTAAAGGCGCGCCAGGGGGCAGCTTAATCAGACCGTCAGCATGGTGCACGTTCTCAATCCTCATAACGTTTCAGCTATTATTCGTACCGCAGATGCCGTTGGCGTACATGAAg          <  1:332675/249‑1 (MQ=255)                                                                                                                                                                                           gTCTGACCGCTCGTGACCGTGTGCATCTGACGAATATCATGCGCAAAATCCGCGTGATGCCAGCCGTGATTAAAGTCACCCGAAACCGCAATTAATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTCGTACCGCAGATGCCGTTGGCGTACATGAAGTTCACGcc  >  1:419407/1‑251 (MQ=255)                                                                                                                                                                                                               gtgCATCTGACGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGACACCCGCAACCGACATTACTGTTTTATGAACCCAACACgatctgc                                                                                                                                    >  1:199842/1‑95 (MQ=255)                                                                                                                                                                                                                 ncATCTGACGAATATCATGCGCAAAATCCGCGTGATGACAGACGTGATTAAAGTCACCCGAAACCGAAATTACTGTTTTCTGAACCCAACACGTTATGCACGCATCTGCGaa                                                                                                                       >  1:56370/2‑112 (MQ=255)                                                                                                                                                                                                                        |                                                                                                                                                                                                                              AGAAGTTTATGGCTGTGGAATGGGATAAAGAGACGGCGCAGGAGTTCATCACCGAAATCAAGGTGGAGATGTTCAATCATCAGGGTGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCATGCGCAAAATCCGCGTGATGCCAGACGTGATTAAAGTCACCCGAAACCGAAATTAATGTTTTATGAACCCAACACGTTATGCACGCATCTGCGAAATGCTCGCCAGGCGGCAGCCTGATCTGACCGTCTGCATGGAGCAGGTCCACAAACCTCATAACGTTTCTGCGATTATTCGTACCGCAGATGCCGTTGGCGTACATGAAGTTCACGCC  >  NC_000913/3824228‑3824664

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑