Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,290,669	G→A	W143* (TGG→TAG)	rssB →	regulator of RpoS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,290,669	0	G	A	95.0%	55.0 / ‑6.1	20	W143* (TGG→TAG)	rssB	regulator of RpoS
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (11/8);  total (11/9)
Fisher's exact test for biased strand distribution p-value = 4.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01

ATGCCACGAATGAACGGGCTTAAACTGCTGGAGCATATACGTAACAGAGGCGACCAGACCCCAGTTCTGGTGATATCTGCCACTGAAAATATGGCAGATATTGCCAAAGCGTTACGTCTGGGCGTTGAAGATGTTTTGCTGAAACCAGTTAAAGATCTGAATCGCTTGCGCGAGATGGTTTTTGCCTGTCTCTATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAATGGTT‑GATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTCAGCAGGTGATTTCCCATTGCCGGGTTAATTATCGTCAATTGGTTGCCGCGGACAAACCCGGCCTGGTGCTTGATATTGCCGCACTTTCGGAAAACGATCTGGCATTTTATTGCCTTGATGTCACCCGAGC  >  NC_000913/1290422‑1290864                                                                                                                                                                                                                                                        |                                                                                                                                                                                                     aTGCCACGAATGAACGGGCTTAAACTGCTGGAGCATATACGTAACAGAGGCGACCAGACCCCAGTTCTGGTGATATCTGCCACTGAAAATATGGCAGATATTGCCAAAGCGTTACGTCTGGGCGTTGAAGATGTTTTGCTGAAACCAGTTAAAGATCTGAATCGCTTGCGCGAGATGGTTTTTGCCTGTCTCTATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTAGGa                                                                                                                                                                                                   <  1:84272/251‑1 (MQ=255)   gCCACGAATGAACGGGCTTAAACTGCTGGAGCATATACGTAACAGAGGCGACCAGACCCCAGTTCTGGTGATATCTGCCACTGAAAATATGGCAGATATTGCCAAAGCGTTACGTCTGGGCGTTGAAGATGTTTTGCTGAAACCAGTTAAAGATCTGAATCGCTTGCGCGAGATGGTTTTTGCCTGTCTCTATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTAGGATg                                                                                                                                                                                                 <  1:157108/251‑1 (MQ=255)   gCCACGAATGAACGGGCTTAAACTGCTGGAGCATATACGTAACAGAGGCGACCAGACCCCAGTTCTGGTGATATCTGCCACTGAAAATATGGCAGATATTGCCAAAGCGTTACGTCTGGGCGTTGAAGATGTTTTGCTGAAACCAGTTAAAGATCTGAATCGCTTGCGCGAGATGGTTTTTGCCTGTCTCTATCCCAGCATGTTTAATTCGCGCGGTGAGGAAGAGGAAAGGCTTTTTCGCGACTAGGATg                                                                                                                                                                                                 <  1:193140/251‑1 (MQ=255)      aCGAATGAACGGGCTTAAACTGCTGGAGCATATACGTAACAGAGGCGACCAGACCCCAGTTCTGGTGATATCTGCCACTGAAAATATGGCAGATATTGCCAAAGCGTTACGTCTGGGCGTTGAAGATGTTTTGCTGAAACCAGTTAAAGATCTGAATCGCTTGCGCGAGATGGTTTTTGCCTGTCTCTATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTAGGATGCaa                                                                                                                                                                                              <  1:579482/251‑1 (MQ=255)                         ctgctgGAGCATATACGTAACAGAGGCGACCAGACCCCAGTTCTGGTGATATCTGCCACTGAAAATATGGCAGATATTGCCAAAGCGTTACGTCTGGGCGTTGAAGATGTTTTGCTGAAACCAGTTAAAGATCTGAATCGCTTGCGCGAGATGGTTTTTGCCTGTCTCTATCCCAGCATGTTTAATTCGCGCGTTGCGGAAGAGGAAAGGCTTTTTCGCGACTAGGATGCAATGGTT‑GATAACCCTGCCGc                                                                                                                                                                          >  1:560183/1‑251 (MQ=255)                                   atatACGTAACAGAGGCGACCAGACCCCAGTTCTGGTGATATCTGCCACTGAAAATATGGCAGATATTGCCAAAGCGTTACGTCTGGGCGTTGAAGATGTTTTGCTGAAACCAGTTAAAGATCTGAATCGCTTGCGCGAGATGGTTTTTGCCTGTCTCTATCCCAGCATGTTTAATTCGCGCGTTGTGGAAGAGGAAAGGCTTTTTCGCGACTAGGATGCAATGGTT‑GATAACCCTGCCGCAGCGGCGaa                                                                                                                                                                 >  2:579870/1‑250 (MQ=255)                                     ataCGTAACAGAGGCGACCAGACCCCAGTTCTGGTGATATCTGCCACTGAAAATATGGCAGATATTGCCAAAGCGTTACGTCTGGGCGTTGAAGATGTTTTGCTGAAACCAGTTAAAGATCTGAATCGCTTGCGCGAGATGGTTTTTGCCTGTCTCTATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTAGGATGCAATGGTT‑GATAACCCTGCCGCAGCGGCGAAatt                                                                                                                                                              <  1:333635/251‑1 (MQ=255)                                     ataCGTAACAGAGGCGACCAGACCCCAGTTCTGGTGATATCTGCCACTGAAAATATGGCAGATATTGCCAAAGCGTTACGTCTGGGCGTTGAAGATGTTTTGCTGAAACCAGTTAAAGATCTGAATCGCTTGCGCGAGATGGTTTTTGCCTGTCTCTATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTAGGATGCAATGGTT‑GATAACCCTGCCGCAGCGGCGAAatt                                                                                                                                                              <  2:509531/251‑1 (MQ=255)                                         gTAACAGAGGCGACCAGACCCCAGTTCTGGTGATATCTGCCACTGAAAATATGGCAGATATTGCCAAAGCGTTACGTCTGGGCGTTGAAGATGTTTTGCTGAAACCAGTTAAAGATCTGAATCGCTTGCGCGAGATGGTTTTTGCCTGTCTCTATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTAGGATGCAATGGTT‑GATACCCCTGCCGCAGCGGCGAAAttatta                                                                                                                                                          <  2:10820/251‑1 (MQ=255)                                                 ggCGACCAGACCCCAGTTCTGGTGATATCTGCCACTGAAAATATGGCAGATCTTGCCAAAGCGTTACGTCTGGGCGTTGAAGATGTTTTGCTGAAACCAGTTAAAGATCTGAATCGCTTGCGCGAGATGGTTTTTGCCTGTCTCTATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTAGGATGCAATGGTT‑GATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACt                                                                                                                                                  >  2:392897/1‑251 (MQ=255)                                                  gCGACCAGACCCGAGTTCTGGTGATCTCTGCCTCTGAAAATATGGCAGATATTGCCAAAGCGTTACGTCTGGGTGTTGAAGATGTTTTTCTGAAACCATTTAAAGATCGGAATCGCTTGCGCGAGATGGTTTTTGCCTGTCTCTTTCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGTAAAGGCTTTTTCGCGACTAGGATGTAATGGTT‑GATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTa                                                                                                                                                 <  1:391374/251‑1 (MQ=255)                                                                                             ggCAGATATTGCCAAAGCGTTACGTCTGGGCGTTGAAGATGTTTTGCTGAAACCAGTTAAAGATCTGAATCGCTTGCGCGAGATGGTTTTTGCCTGTCTCTATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTAGGATGCAATGGTT‑GATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTCAGCAGGTGATTTCCCATTGCCGGGTTCAtt                                                                                                      >  1:299748/1‑251 (MQ=255)                                                                                              gCAGATCTTGCAAAAGCGTTACGTCTGGGCGTTGCAGATGTTTTGCTGAAACCAGTTAAAGATCTGAATCGATTGCGCGAGATGGTTTTTGCCTGTCTCTATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTAGGATGCAATGGTT‑GATAACCCTGCCGCAGCGGCGAAATTATTCCAGGAACTACAAACGCCGGTTCAGCAGGCGATTTCCCATTGCCGGGTTAAtt                                                                                                      >  2:393975/1‑250 (MQ=255)                                                                                                      tGCCAAAGCGTTACGTCTGGGCGTTGAAGATGTTTTGCTGAAACCAGTTAAAGATCTGAATCGCTTGCGCGAGATGGTTTTTGCCTGTCTCTATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTAGGATGCAATGGTT‑GATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTCAGCAGGTGATTTCCAATTGCCGGGTTAATTATCGTCAAt                                                                                             >  2:70366/1‑251 (MQ=255)                                                                                                                                                  cAGTTAAAGATCTGACTCGCTTGCGCGAGATGGTTTTTGCCTGTCTCTATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTAGGATGCAATGGTT‑GATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTCAGCAGGTGATTTCCCATTGCCGGGTTAATTATCGTCAATTGGTTGCCGCGGACAAACCCGGCCTGGTGCTTGCTATTGCCGc                                                  >  2:66063/1‑250 (MQ=255)                                                                                                                                                                      ttGCGCGAGATGGTTTTTGCCTGTCTCTATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTAGGATGCAATGGTT‑GATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTCAGCAGGTGATTTCACATTGCCGGGTTAATTATCGTCAATTGGTTGCCGCGGACAAACCCGGCCTGGTGCTTGATATTGCCGCACTTTCGGAAAACGATCTGGc                             >  2:185749/1‑251 (MQ=255)                                                                                                                                                                       tGCGCGAGATGGCATTTGCCTGTCTATATACCAGCACGTTTAATTAGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTAGGATGCAATGGTT‑GATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAAACGCCGGTTCAGCAGGTGATTTCCCATTGCCGGGGTAATTATCGTCAATTGGTTGCCGCGGTCAACCCCGGCCTGGTGCTTGCTGTTGCCGCACTTTCGGAAACAGATCTGGc                             >  2:275512/1‑250 (MQ=255)                                                                                                                                                                            gagaTGGTTTTTGCCTGTCTCTATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTAGGATGCAATGGTT‑GATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTCAGCAGGTGATTTCCCATTGCCGGGTTACTTATCGTCAATTGGTTGCCGCGGACAAACCCGGCCTGGTGCTTGATATTGCCGCACTTTCGGAAAACGATCTGGCAttttt                       >  2:411274/1‑250 (MQ=255)                                                                                                                                                                                                 actcccagattttttAAGTCGCGTGTGGAGGAAGAGGAATGTTTTTCTGGCTACTGGGATG‑AATGTTTTAATACCCCTGCCGCAGCGGCAAAATTATTAAAGGAACTACAGCCGCCGGTTCAGCAGGTGATTTCCCATTGCCGGGTTAATTATCGTCAATTGGTTGCCGCGGACAAACCCGGCCTGGTGCTTGATATTGCCGCACTTTCGGAAAACGATCTGGCATTTTATTGCCTTGATGTCACCCGAGc  <  1:264907/239‑1 (MQ=255)                                                                                                                                                                                                    cccAGCATGTTTAATGAGCGCGTTGAGGCTGCGGAAAGGCTTTTTCGCGACTAGGATGCACTGGTT‑GCTAACCATGCCGCAGCGGCGCAATTATTACCGGAACTACAACCGCCGGTTCAGCAGGTGATTTCCCATTGCCgg                                                                                                             >  2:332891/1‑141 (MQ=255)                                                                                                                                                                                                                                                        |                                                                                                                                                                                                     ATGCCACGAATGAACGGGCTTAAACTGCTGGAGCATATACGTAACAGAGGCGACCAGACCCCAGTTCTGGTGATATCTGCCACTGAAAATATGGCAGATATTGCCAAAGCGTTACGTCTGGGCGTTGAAGATGTTTTGCTGAAACCAGTTAAAGATCTGAATCGCTTGCGCGAGATGGTTTTTGCCTGTCTCTATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAATGGTT‑GATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTCAGCAGGTGATTTCCCATTGCCGGGTTAATTATCGTCAATTGGTTGCCGCGGACAAACCCGGCCTGGTGCTTGATATTGCCGCACTTTCGGAAAACGATCTGGCATTTTATTGCCTTGATGTCACCCGAGC  >  NC_000913/1290422‑1290864

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑