Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,134,669	T→A	8.0%	intergenic (+112/‑60)	flgF → / → flgG	flagellar component of cell‑proximal portion of basal‑body rod/flagellar component of cell‑distal portion of basal‑body rod

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,134,669	0	T	A	8.0%	172.8 / 5.3	50	intergenic (+112/‑60)	flgF/flgG	flagellar component of cell‑proximal portion of basal‑body rod/flagellar component of cell‑distal portion of basal‑body rod
Reads supporting (aligned to +/- strand):  ref base T (24/22);  new base A (2/2);  total (26/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.06e-01

ACCAACTGCTGTCGATGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATGATCAGTTCATTATGGATCGCCAAAACGGGCCTTGACGCCCAGCAAACCAATATGGACGTCATTGCCAACAACCTGGCAAACGTC  >  NC_000913/1134535‑1134815                                                                                                                                       |                                                                                                                                                   accaacTGCTGTCGATGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATGCGGCGTAAAcgcctta                                                                                                                                            <  2:538717/143‑4 (MQ=255) accaacTGCTGTCGATGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATGCGGCGTAAAcgcctta                                                                                                                                            >  1:538717/1‑140 (MQ=255)      ctgctgTCGATGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTa                                                                                                                                                   >  2:827003/1‑131 (MQ=255)      ctgctgTCGATGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTa                                                                                                                                                   <  1:827003/131‑1 (MQ=255)                        ttGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTAcg                                                                                                                                                 <  2:692058/115‑1 (MQ=255)                        ttGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTAcg                                                                                                                                                 >  1:692058/1‑115 (MQ=255)                         tGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATGCGGCGTAAAcgcct                                                                                                                                              >  1:924887/1‑116 (MQ=255)                         tGAAAGGATACATGACAAGCATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATGCGGCGTAAAcgcct                                                                                                                                              <  2:924887/117‑2 (MQ=255)                          gAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCAc                                                                                                              >  1:609409/1‑148 (MQ=255)                           aaaGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACttt                                                                                                                   <  4:303503/142‑1 (MQ=255)                           aaaGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACttt                                                                                                                   >  3:303503/1‑142 (MQ=255)                                     tGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATACACTAc                                                                                                   <  2:609409/148‑1 (MQ=255)                                                aGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTAcg                                                                                                                                                 >  1:1079668/1‑91 (MQ=255)                                                aGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTAcg                                                                                                                                                 <  2:1079668/91‑1 (MQ=255)                                                  ttGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTAcg                                                                                                                                                 >  2:1007152/1‑89 (MQ=255)                                                  ttGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTAcg                                                                                                                                                 <  1:1007152/89‑1 (MQ=255)                                                  ttGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACata                                                                                                                           <  3:695717/111‑1 (MQ=255)                                                  ttGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACata                                                                                                                           >  4:695717/1‑111 (MQ=255)                                                       cGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGTAGACATATGCACTTTGTCACTAAt                                                                                                          >  3:713386/1‑123 (MQ=255)                                                       cGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAAt                                                                                                          <  4:713386/123‑1 (MQ=255)                                                              cAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGttt                                                                                                                                                    <  1:614779/74‑1 (MQ=255)                                                              cAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGttt                                                                                                                                                    >  2:614779/1‑74 (MQ=255)                                                              cAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACt                                                                                                     <  4:214138/121‑1 (MQ=255)                                                              cAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACt                                                                                                     >  3:214138/1‑121 (MQ=255)                                                                  tttATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATGATCAGTTc                                                                              <  3:992741/140‑1 (MQ=255)                                                                  tttATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATGATCAGTTc                                                                              >  4:992741/1‑140 (MQ=255)                                                                                 ggggCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTg                                                                                                                  >  1:24647/1‑89 (MQ=255)                                                                                 ggggCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTg                                                                                                                  <  2:24647/89‑1 (MQ=255)                                                                                  gggCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCa                                                                                                                                     >  4:571390/1‑69 (MQ=255)                                                                                  gggCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCa                                                                                                                                     <  3:571390/69‑1 (MQ=255)                                                                                     cAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCa                                                                                                                       >  2:902192/1‑80 (MQ=255)                                                                                     cAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCa                                                                                                                       <  1:902192/80‑1 (MQ=255)                                                                                         cGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATGAt                                                                                    <  1:33175/111‑1 (MQ=255)                                                                                         cGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATGAt                                                                                    >  2:33175/1‑111 (MQ=255)                                                                                           cAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCg                                                                                                                                        >  3:384776/1‑57 (MQ=255)                                                                                           cAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCg                                                                                                                                        <  4:384776/57‑1 (MQ=255)                                                                                             aTTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATGAt                                                                                    >  2:888050/1‑107 (MQ=255)                                                                                             aTTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATGAt                                                                                    <  1:888050/107‑1 (MQ=255)                                                                                              tttATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAAt                                                                                                          >  4:475835/1‑84 (MQ=255)                                                                                              tttATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAAt                                                                                                          <  3:475835/84‑1 (MQ=255)                                                                                                                         ccGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACAtt                                                                                           <  2:685930/72‑1 (MQ=255)                                                                                                                         ccGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACAtt                                                                                           >  1:685930/1‑72 (MQ=255)                                                                                                                            gATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATGATCAg                                                                                 >  3:910027/1‑79 (MQ=255)                                                                                                                            gATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATGATCAg                                                                                 <  4:910027/79‑1 (MQ=255)                                                                                                                              tAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATGATCAGTTCATTATGGATCGCCAAAACGGGCCTTGACGCCCAGCAAACCAATATGGACGTCATTGCCAACAACCTgg          >  4:265743/1‑148 (MQ=255)                                                                                                                                aGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATGATCAGTTCATTATGGATCGCCAAAACGGACCTTGACGCCCAGCAAACCAATATGGACGTCATTGCCAACAACCTGGCa        >  2:85239/1‑148 (MQ=255)                                                                                                                                 ggCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACt                                                                                                     >  3:892272/1‑54 (MQ=255)                                                                                                                                 ggCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACt                                                                                                     <  4:892272/54‑1 (MQ=255)                                                                                                                                  gCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATg                                                                                      <  1:686286/68‑1 (MQ=255)                                                                                                                                  gCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATg                                                                                      >  2:686286/1‑68 (MQ=255)                                                                                                                                  gCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATGATCAGTTCATTATGGATCGCCAAAACg                                                           >  4:346092/1‑95 (MQ=255)                                                                                                                                  gCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATGATCAGTTCATTATGGATCGCCAAAACg                                                           <  3:346092/95‑1 (MQ=255)                                                                                                                                     tttACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATGATCAGTTCATTATGGATCGCCAAAACGGGCCTTGACGCCCAGCAAACCAATATGGACGTCATTGCCAACAACCt            <  2:471599/139‑1 (MQ=255)                                                                                                                                     tttACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATGATCAGTTCATTATGGATCGCCAAAACGGGCCTTGACGCCCAGCAAACCAATATGGACGTCATTGCCAACAACCt            >  1:471599/1‑139 (MQ=255)                                                                                                                                     tttACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATGATCAGTTCATTATGGATCGCCAAAACGGGCCTTGACGCCCAGCAAACCAATATGGACGTCATTGCCAACAACCTGGCAAACGt   <  1:85239/148‑1 (MQ=255)                                                                                                                                      ttACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATGATCAGTTCATTATGGATCGCCAAAACGGGCCTTGACGCCCAGCAAACCAATATGGACGTCATTGCCAACAACCTGGCAAACGTc  >  4:769249/1‑148 (MQ=255)                                                                                                                                       |                                                                                                                                                   ACCAACTGCTGTCGATGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCACTAATCCACTACAGGACATTTTATGATCAGTTCATTATGGATCGCCAAAACGGGCCTTGACGCCCAGCAAACCAATATGGACGTCATTGCCAACAACCTGGCAAACGTC  >  NC_000913/1134535‑1134815

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑