Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,130,803	C→T	A21T (GCG→ACG)	flgA ←	flagellar basal body P‑ring formation protein FlgA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,130,803	0	C	T	94.4%	49.4 / ‑4.0	18	A21T (GCG→ACG)	flgA	flagellar basal body P‑ring formation protein FlgA
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (8/9);  total (8/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.53e-01

CAACCACATAATTTCCTGTGGCCTGTACATTAACCTGTAAATATCGTTTGTCGTTACCGCAGCGTGCCAACACATTCACATTGCCCCACAGGCGGGAATTATTGCTCATCGAAAGCAATGGCTGCTCGCATGGCGGTAGTAGATTGGGCGCTGTACGAATAGAAACACGAACCTCATCACTTACCCCCGCGAGTTGGGCGCTAAAAAAGTTGTGCAATTGCGATGTGAGATTGCTCGCCGTACTTAACGGACTGAACAGTATCGCGATGATCGCCACGCTACGTTTTATTATCAGCATTTTCGCCCCCAGCCATTTCTACAACGTGAATTGTACCTGTCCGCAATGACCATCAACGGCATAAATAGCGACCCATTTTGCGTTTATTCCGCCGATAACGCGCGCGTAAAGGCATTTAAGCTGATGGCAGAATTTTGATACCTGCGGAGGAGATATGCTCGATAAGCTCGACGCC  >  NC_000913/1130566‑1131038                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                            cAACCACATAATTTCCTGTGGCCTGTACATTAACCTGTAAATATCGTTTGTCGTTACCGCAGCGTGCCAACACATTCACATTGCCCCACAGGCGGGAATTATTGCTCATCGAAAGCAATGGCTGCTCGCATGGCGGTAGTAGATTGGGCGCTGTACGAATAGAAACACGAACCTCATCACTTACCCCCGCGAGTTGGGCGCTAAAAAAGTTGTGCAATTGCGATGTGAGATTGCTCGTCGTACTTAACGGa                                                                                                                                                                                                                                <  1:37404/251‑1 (MQ=255)             ttCCTGTGGCCTGTACATTAACCTGTAAATATCGTTTGTCGTTACCGCAGCGTGCCAACACATTCACATTGCCCCACAGGCGGGAATTATTGCTCATCGAAAGCAATGGCTGCTCGCATGGCGGTAGTAGATTGGGCGCTGTACGAATAGAAACACGAACCTCATCACTTACCCCCGCGAGTTGGGCGCTAAAAAAGTTGTGCAATTGCGATGTGAGATTGCTCGTCGTACTTAACGGACTGAACAGTAt                                                                                                                                                                                                                     <  1:292944/250‑1 (MQ=255)                                     gTAAATATCGTTTGTCGTTACCGCAGCGTGCCAACACATTCACATTGCCCCACAGGCGGGAATTATTGCTCATCGAAAGCAATGGCTGCTCGCATGGCGGTAGTAGATTGGGCGCTGTACGAATAGAAACACGAACCTCATCACTTACCCCCGCGAGTTGGGCGCTAAAAAAGTTGTGCAATTGCGATGTGAGATTGCTCGTCGTACTTAACGGACTGAACAGTATCGCGATGATCGCCACGCTACGtttt                                                                                                                                                                                            <  1:284325/251‑1 (MQ=255)                                       aaaTATCGTTTGTCGTTACCGCAGCGTGCCAACACATTCACATTGCCCCACAGGCGGGAATTATTGCTCATCGAAAGCAATGGCTGCTCGCATGGCGGTAGTAGATTGGGCGCTGTACGAATAGAAACACGAACCTCATCACTTACCCCCGCGAGTTGGGCGCTAAAAAAGTTGTGCAATTGCGATGTGAGATTGCTCGTCGTACTTAACGGACTGAACAGTATCGCGATGATCGCCACGCTACGTTtta                                                                                                                                                                                           <  1:40632/250‑1 (MQ=255)                                        aaTATCGTTTGTCGTTACCGCAGCGTGCCAACACATTCACATTGCCCCACAGGCGGGAATTATTGCTCATCGAAAGCAATGGCTGCTTGCATGGCGGTAGTAGATTGGGCGCTGTACGAATAGAAACACGAACCTCATCACTTACCCCCGCGAGTTGGGCGCTAAAAAAGTTGTGCAATTGCGATGTGAGATTGCTCGCCGTACTTAACGGACTGAACAGTATCGCGATGATCGCCACGCTACGTTttatt                                                                                                                                                                                         <  1:77890/251‑1 (MQ=255)                                                                   ccAACACATTCACATTGCCCCACAGGCGGGAATTATTGCTCATCGAAAGCAATGGCTGCTCGCATGGCGGTAGTAGATTGGGCGCTGTACGAATAGAAACACGAACCTCATCACTTACCCCCGCGAGTTGGGCGCTAAAAAAGTTGTGCAATTGCGATGTGAGATTGCTCGTCGTACTTAACGGACTGAACAGTATCGCGATGATCGCCACGCTACGTTTTATTATCAGCATTTGCGCCCCCAGCCATTTc                                                                                                                                                              <  1:313031/251‑1 (MQ=255)                                                                         cattcacattGCCCCACAGGCGGGAATTATTGCTCATCGAAAGCAATGGCTGCTCGCATGGCGGGAGTAGATTGGGCGCTGTACGAATAGAAAAACGAACCTCATCCCTTACCCCCGCGAGGTGGGGGCTAAAAAAATTGTGCAAATGCGATGTGGGATTGGTCGTCGTACTTAACGGGCTGAACAGTATCGCGATGATCGCCACGCTACGTTTTTTTTTCAGCATTTTTTCCCCCCACCCTTTCTACAAc                                                                                                                                                        >  1:248021/1‑251 (MQ=255)                                                                             cacattGCCCCGCAGGCGGGAATTATTGCTCATCGAAAGCAATGGCTGCTCGCATGGCGGTAGTAGATTGGGCGCTGTACGAATAGAAACACGAACCTCATCACTTACCCCCGCGAGTTGGGCGCTAAAAAAGTTGTGCAATTGCGATGTGAGATTGCTCGTCGTACTTAACGGACTGAACAGTATCGCGATGATCGCCACGCTACGTTTTATTATCAGCATTTTCGCCCCCAGCCATTTCTACAACGTg                                                                                                                                                     <  1:177472/250‑1 (MQ=255)                                                                                            gCGGGAATTATTGCTCATCGAAAGCAATGGCTGCTCGCATGGCGGTAGTAGATTGGGCGCTGTACGAATAGAAACACGAACCTCATCACTTACCCCCGCGAGTTGGGCGCTAAAAAAGTTGTGCAATTGCGATGTGAGATTGCTCGTCGTACTTAACGGACTGAACAGTATCGCgatgat                                                                                                                                                                                                            >  2:65803/1‑180 (MQ=255)                                                                                            gCGGGAATTATTGCTCATCGAAAGCAATGGCTGCTCGCATGGCGGTAGTAGATTGGGCGCTGTACGAATAGAAACACGAACCTCATCACTTACCCCCGCGAGTTGGGCGCTAAAAAAGTTGTGCAATTGCGATGTGAGATTGCTCGTCGTACTTAACGGACTGAACAGTATCGCgatgat                                                                                                                                                                                                            <  1:65803/180‑1 (MQ=255)                                                                                                     attGCTCATCGAAAGCAATGGCTGCTCGCATGGCGGTAGTAGATTGGGCGCTGTACGAATAGAAACACGAACCTCATCACTTACCCCCGCGAGTTGGGCGCTAAAAAAGTTGTGCAATTGCGATGTGAGATTGCTCGTCGTACTTAACGGACTGAACAGTATCGCGATGATCGCCACGCTACGTTTTATTATCAGCATTTTCGCCCCCAGCCATTTCTACAACGTGAATTGTAACTGTCCGAAATGACCAt                                                                                                                            >  2:129158/1‑251 (MQ=255)                                                                                                                  aGCAATGGCTGCTCGCATGGCGGTAGTAGATTGGGCGCTGTACGAATAGAAACACGAACCTCATCACTTACCCCCGCGAGTTGGGCGCTAAAAAAGTTGTGCAATTGCGATGTGAGATTGCTCGTCGTACTTAACGGACTGAACAGTATCGCGATGATCGCCACGCTACGTTTTATTATCAGCATTTTCGCCCCCAGCCATTTCTACAACGTGAATTGTACCTGTCCGCAATGACCATCAACGGCATAAAt                                                                                                               <  1:192549/251‑1 (MQ=255)                                                                                                                             ctCGCATGGCGGTAGTAGATTGGGCGCTGTACGAATAGAAACACGAACCTCATCACTTACCCCCGCGAGTTGGGCGCTAAAAAAGTTGTGCAATTGCGATGTGAGATTGCTCGTCGTACTTAACGGACTGAACAGTATCGCGATGATCGCCACGCTACGTTTTATTATCAGCATTTTCGCCCCCAGCCATTTCTACAACGTGAATTGTACCTGTCCGCAATGACCATCAACGGCATAAATAGCGACCCAtt                                                                                                    >  1:222648/1‑251 (MQ=255)                                                                                                                                              aaTTGGGCGCTGTACGAATAGAAACACGAACCTCATCACTTACCCCCGCGAGTTGGGCGCTAAAAAAGTTGTGCAATTGCGATGTGAGATTGCTCGTCGTACTTAACGGACTGAACAGTATCGCGATGATCGCCACGCTACGTTTTATTATCAGCATTTTCGCCCCCAGCCATTTCTACAACGTGAATTGTACCTGTCCGCAATGACCATCAACGGCATAAATAGCGACCCATTTTGCGTTTATTccgccg                                                                                   <  1:150079/250‑1 (MQ=255)                                                                                                                                                                                         ccccGCGAGTTGGGCGCTAAAAAAGTTGTGCAATTGCGATGTGAGATTGCTCGTCGTACTTAACGGACTGAACAGTATCGCGATGATCGCCACGCTACGTTTTATTATCAGCATTTTCGCCCCCAGCCATTTCTACAACGTGAATTGTACCTGTCCGCAATGACCATCAACGGCATAAATAGCGACCCATTTTGCGTTTATTCCGCCGATAACGCGCGCGTAAAGGCATTTAAGCTGATGGCAGAATTTTg                                        >  1:10939/1‑251 (MQ=255)                                                                                                                                                                                                 gTTGGGCGCTAAAAAAGTTGTGCAATTGCGATGTGAGATTGCTCGTCGTACTTAACGGACTGAACAGTATCGCGATGATCGCCACGCTACGTTTTATTATCAGCATTTTCGCCCCCAGCCATTTCTACAACGTGAATTGTACCTGTCCGCAATGACCATCAACGGCATAAATAGCGACCCATTTTGCGTTTATTCCGCCGATAACGCGCGCGTAAAGGCATTTAAGCTGATGGCAGAATTTTGATACCTGc                                >  1:109724/1‑251 (MQ=255)                                                                                                                                                                                                      gcgcTAAAAAAGATGTGCAATTGCGATGTGAGATTGCTCGTCGTACTTAACGGACTGAACAGTATCGCGATGATCGCCACGCTACGTTTTATTATCAGCATTTTCGCCCCCAGCCATTTCTACAACGTGAATTGTACCTGTCCGCAATGACCATCAACGGCATAAATAGCGACCCATTTTGCGTTTATTCCGCCGATAACGCGCGCGTAAAGGCATTTAAGCTGATGGCAGAATTTTGATACCTGCggagg                           >  1:7106/1‑251 (MQ=255)                                                                                                                                                                                                                               aTGTGAGATTGCTCGTCGTACTTAACGTACTGAACAGTATCGCGATGATCGCCACGCTACGTTTTATTATCAGCATTTTCGCCCCCAGCCATTTCTACAACGTGAATTGTACCTGTCCGCAATGACCATCAACGGCATAAATAGCGACCCATTTTGCGTTTATTCCGCCGATAACGCGCGCGTAAAGGCATTTAAGCTGATGGCAGAATTTTGATACCTGCGGAGGAGCTATGCTCGATAAGCTCGAcgcc  >  1:280301/1‑251 (MQ=255)                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                            CAACCACATAATTTCCTGTGGCCTGTACATTAACCTGTAAATATCGTTTGTCGTTACCGCAGCGTGCCAACACATTCACATTGCCCCACAGGCGGGAATTATTGCTCATCGAAAGCAATGGCTGCTCGCATGGCGGTAGTAGATTGGGCGCTGTACGAATAGAAACACGAACCTCATCACTTACCCCCGCGAGTTGGGCGCTAAAAAAGTTGTGCAATTGCGATGTGAGATTGCTCGCCGTACTTAACGGACTGAACAGTATCGCGATGATCGCCACGCTACGTTTTATTATCAGCATTTTCGCCCCCAGCCATTTCTACAACGTGAATTGTACCTGTCCGCAATGACCATCAACGGCATAAATAGCGACCCATTTTGCGTTTATTCCGCCGATAACGCGCGCGTAAAGGCATTTAAGCTGATGGCAGAATTTTGATACCTGCGGAGGAGATATGCTCGATAAGCTCGACGCC  >  NC_000913/1130566‑1131038

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑