Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,867,455	G→A	Q33* (CAG→TAG)	rpoS ←	RNA polymerase sigma factor RpoS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,867,455	0	G	A	90.0%	16.2 / ‑5.9	10	Q33* (CAG→TAG)	rpoS	RNA polymerase sigma factor RpoS
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (4/5);  total (4/6)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.15e-01

GCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGT  >  NC_000913/2867231‑2867556                                                                                                                                                                                                                                 |                                                                                                      gcggGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGCGGCGACCTCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCt                                                                                         >  1:228595/1‑239 (MQ=255)               ccaccaGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGATTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTGAGCACGTGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtc                                                               <  1:226514/251‑1 (MQ=255)                                           ccGGCGGAGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCACAATAAACTTGTTCTTCAACCGTTAACAGTGGTGAATAACCAATCTCACCCAGGTAAACCTAAGTCGCGTCCACCACACGCCGTGTGTCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGATTCCTATTCTACTAAGACCTTTTCGTCAAACACCTAAACTACGTTCTCCTCAAATTCCGCATATTCATTTAAAt                                   >  1:237418/1‑251 (MQ=255)                                               cggcgAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGGCGCGTCCAACACACGCTGTGTGGCTCCCGGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACGGCGTTCTCATCAAATTCCGCATCTTCATTTAAATCAtn                               <  1:72721/251‑2 (MQ=255)                                                                   ccNNAGTGNGCGACGCGCAAAATAAACTTCTTCNTCGGCCGTTAACAGTGGTGAATAACCAATCTNCNCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGNTAACAGTTCCNCTTNNGCCANANCNTTATCACTGGGTTCCTATTCTACTAAGGCNTTTTCGTCAAAAACCTCAACTCCNNTCNNNTCNNATTcc                                                   <  2:263641/210‑1 (MQ=255)                                                                       cgTGCGCGACGCGCAAAATAATCTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGTTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAAGCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATGCCGCATCTTCATTTAAATCATGACCTTTCAGCGTATTCTGACTCAt       <  1:16085/250‑1 (MQ=255)                                                                        gTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCAt       >  1:110342/1‑250 (MQ=255)                                                                           cgcgACGCGCAAAATAAACTGCTTCTTCGGCCGTTAACAGTGGGGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTACGACAACAGTTCCCCATCGGCAAAATCGTATTCACGGTGTTCCTGTTCTACGAAGGCCTGGACGTCAAAATACTAATCTGCGTTAGCAACAAAGTCCGCATCTTAATTTAAATCATGACCTTTCAGCGTAGTATGAATCATAAgg   <  1:344245/251‑1 (MQ=255)                                                                            gcgACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGCAAAGCTGAGTCGCGTCCCACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCCCTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTAAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGt  >  1:180920/1‑251 (MQ=255)                                                                                                                             ccAATCTCGCCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCTCTGCGATAACAGTTCCTCTTCGGCCAAATCTGTATCACTGGGTTCGTATTCTACTAAGTCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGa                              <  1:305188/174‑1 (MQ=255)                                                                                                                                                                                                                                 |                                                                                                      GCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGT  >  NC_000913/2867231‑2867556

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑