Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	1,999,185	C→A	19.9%	D134E (GAC→GAA)	fliS →	flagellar protein potentiates polymerization

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	1,999,185	0	C	A	19.9%	45.2 / 3.0	20	D134E (GAC→GAA)	fliS	flagellar protein potentiates polymerization
Reads supporting (aligned to +/- strand):  ref base C (7/9);  new base A (2/2);  total (9/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.75e-01

ATCAGCAAGGCAAAGGCGTCTCTTTGTCAAAAGCGATCAACATCATTGAGAACGGACTGCGGGTGAGTCTTGATGAAGAGAGCAAAGACGAACTAACCCAAAACTTGATTGCTCTTTATAGCTATATGGTCAGGCGCTTGCTGCAAGCCAATTTACGCAACGATGTCTCCGCAGTCGAAGAAGTGGAAGCATTAATGCGCAATATTGCCGATGCCTGGAAAGAGTCGTTACTCTCCCCTTCTTTGATTCAGGACCCAGTCTGATGAACCATGCACCGCATTTATATTTCGCCTGGCAACAACTCGTCGAAAAAAGCCAGCTCATGTTACGCCTGGCAACGGAAGAACAATGGGACGAACTCATCGCCAGCGAAATGGCGTATGTGAATGCGGTGCAGGAGATTGCACATTTGACTGAAGAGGTTGACCCGTCCACCACGATGCAGGAGC  >  CP009273/1998932‑1999380                                                                                                                                                                                                                                                              |                                                                                                                                                                                                    aTCAGCAAGGCAAAGGCGTCTCTTTGTCAAAAGCGATCAACATCATTGAGAACGGACTGCGGGTGAGTCTTGATGAAGAGAGCAAAGACGANCTAACCCAAAACTTGATTGCTCTTTATAGCTATATGGTCAGGCGCTTGCTGCAAGCCAATTTACGCAACGATGTCTCCGCAGTCGAAGAAGTGGAAGCATTAATGCGCAATATTGCCGATGCCTGGAAAGAGTCGTTATCCTCCCCTTCTTTGATTCAGGACCCAGTCTGATGAACCATGCAc                                                                                                                                                                                <  1:376496/275‑1 (MQ=255)                                                                  aGTCTTGATGAAGAGAGCAAAGACGAACTAACCCAAAACTTGATTGCTCTTTATAGCTATATGGTCAGGCGCTTGCTGCAAGCCAATTTACGCAACGATGTCTCCGCAGTCGAAGAAGTGGAAGCATTAATGCGCAATATTGCCGATGCCTGGAAAGAGTCGTTACTCTCCCCTTCTTTGATTCAGGAACCAGTCTGATGAACCATGCACCGCATTTATATTTCGCCTGGCAACAACTCGTCGAAAAAAGACAGCGCATGTTACGCCTggtcac                                                                                                                >  2:187117/1‑270 (MQ=255)                                                                              gagagCAAAGACGAAATAACCCAGGACTGGATTGCTCTTTATAGCTATATGGTCAGGCGCTTGCTGCAAGCCAATTTACGCAACGATGTCTCCGCAGTCGAAGAAGTGGAAGCATTAATGCGCAATATTGCCGATGCCTGGAAAGAGTCGTTACTCTCCCCTTCTTTGATTCAGGACCCAGTCNGATGAACCATGCACCGCATTTATATTTCGCCTGGCAACAACTAGTCGAAAAAAGCCAGCTCATGTTACACCTGGCAACGGAAGAACAATg                                                                                                    >  1:359696/1‑274 (MQ=255)                                                                                                 cccAAAACTTGATTGCTCTTTATAGCTATATGGTCAGGCGCTTGCTGCAAGCCAATTTACGCAACGATGTCTCCGCAGTCGAAGAAGTGGAAGCATTAATGCGCAATATTGCCGATGCCTGGAAAGAGTCGTTACTCTCCCCTTCTTTGATTCAGGACCCa                                                                                                                                                                                                  <  2:364048/161‑1 (MQ=255)                                                                                                                             tatGGTCAGGCGCTTGCTGCAAGCCAATTTACGCAACGATGTCTCCGCAGTCGAAGAAGTGGAAGCATTAATGCGCAATATTGCCGATGCCTGGAAAGAGTCGTTACTCTCCCCTTCTTTGATTCAGGACCCAGTCTGATGAACCATGCAACGCATTTATATTTCGCCTGGCAACAACTCGTCGAAAAAAGCCAGCTCATGTTACGCCTGGCAACGGAAGAACAAAGGTACGAACTCATCGCCAGCGAAAAGGCGCATGTGAATGCGGTGCAGga                                                    >  1:50904/1‑275 (MQ=255)                                                                                                                             tatGGTCAGCANTTTGCTGCACGCCAATTTACGCAACGATGTCTCCGCAGTCGAAGAAGTGGAAGCATTAATGCGCAATATTGCCGATGCCTGGAAAGAGTCGTTACTCTCCCCTTCTTTGATTCAGGACCCAGTCTGATGAACCATGCACCGCATTTATATTTCGCCTGGCAACAACTCGTCGAAAAAAGCCAGCTCATGTTACGCCTGGCAACGGAAGAACAATGGGACGAACTCATCGCCAGCGAAATGGCGTATGTGAATGCGGTGCAGga                                                    <  2:50904/275‑1 (MQ=255)                                                                                                                                 gTCAGGCGCTTGCTGCAAGCCAATTTACGCAACGATGTCTCCGCAGTCGAAGAAGTGGAAGCATTAATGCGCAATATTGCCGATGCCTGGAAAGAGTCGTTACTCTCCCCTTCTTTGATTCAGGACCCa                                                                                                                                                                                                  <  1:410132/129‑1 (MQ=255)                                                                                                                                                cAAGCCAATTTACTCTACGATGTCTCCGCAGTTGAAGAAGTGGAAGCATTAATACACAATATTGCCGATGCCTGTGAAGAGTCGTTACTCTCCCCTTCTTTGATTCAGGAACCAGTCTGATGTACCATGCAACGCATTTATATTTCGCCTGGCAACAACTCGTCGAAAAAAGCCAGCTCATGTTACGCCTGGCAACGGAAGAACAATGGGACGAACTCATCGCCAGCGAAATGGCGTATGTGAATGCGGTGCAGGGGATTGCACATTTGACTGa                                  <  1:187124/274‑1 (MQ=255)                                                                                                                                                                         gacaaGTGGAAGAGGTGGAAGGATTATTTCGCAATATTGCCGATGCCTGGATAGAGTCGTTACTCTCCCCTTCTTTGATTCAGGACCCAGTCTGATGAACCATGCACCGCATTTATATTTCGCCTGGCAACAACTCGTCGAAAAAAGCCAGCTCATGTTACGCCTGGCAACGGAAGAACAATGGGACGAACTCATCGCCAGCGAAATGGCGTATGTGAATGCGGTGCAGGAGATTGCACATTTGACTGAAGAGGTTGACCCGTCCACCACGATGc        <  2:359684/271‑1 (MQ=255)                                                                                                                                                                                                     gcgcAATATTGCCGATGCCTGGAAAGAGTCGTTACTCTCCCCTTCTTTGATTCAGGACCCa                                                                                                                                                                                                  <  2:110255/61‑1 (MQ=255)                                                                                                                                                                                                           tatTGCCGATGCCTGGAAAGAGTCGTTACTCTCCCCTTCTTTGATTCAGGACCCAGTCTGATGAACCATGc                                                                                                                                                                                  >  2:196286/1‑71 (MQ=255)                                                                                                                                                                                                               gCCGATGCCTGGAAAGAGTCGTTACTCTCCCCTTCTTTGATTCAGGACCCAGTCTGATGAACCATGCACCg                                                                                                                                                                              <  1:196293/71‑1 (MQ=255)                                                                                                                                                                                                                     gCCTGGAAAGAGTCGTTACTCTCCCCTTCTTTGATTCAGGACCCAGTCTGATGAACCATGCACCGCATTTATATTTCGCCTGGCAACAACTCGTCGAAAAAAGCCAGCTCATGTTACGCCTGGCAACGGAAGAACAATGGGACGAACTCATc                                                                                       >  1:430190/1‑152 (MQ=255)                                                                                                                                                                                                                         ggAAAGAGTCGTTACTCTCCCCTTCTTTGATTCAGGACCCAGTCTGATGAACCATGCACCGCATTTATATTTCGCCTGGCAACAACTCGTCGAAAAAAGCCAGCTCATGTTACGCCTGGCAACGGAAGAACAATGGGACGAACTCATCGCCa                                                                                   <  2:430175/152‑1 (MQ=255)                                                                                                                                                                                                                               agTCGTTACTCTCCCCTTCTTTGATTCAGGACCCAGTCTGATGAACCATGCACCGCATTTATATTTCGCCTGGCAACAACTCGTCGAAAAAAGCCAGCTCATGTTACGCCTGGCAACGGAAGAACAATGGGACGAACTCATCGCCAGCGAAATGGCGTATGTGAATGCGGTGCAGGAGATTGCACATTTGACTGAAGAGGTTGACCCGTCCACCACGATGCAGGagc  >  1:295296/1‑227 (MQ=255)                                                                                                                                                                                                                                      aCTCTCCCCTTCTTTGATTCAGGAACCAGTCTGATGAACCATGCACCGCATTTATATTTCGCCTGGCAACAACTCGTCGAAAAAAGCCAGCTCATGTTACGCCTGGCAACGGAAGAACAATGGGACGAACTCATCGCCAg                                                                                  >  1:153174/1‑140 (MQ=255)                                                                                                                                                                                                                                          tcCCCTTCTTTGATTCAGGAACCAGTCTGATGAACCATGCACCGCATTTATATTTCGCCTGGCAACAACTCGTCGAAAAAAGCCAGCTCATGTTACGCCTGGCAACGGAAGAACAATGGGACGAACTCATCGCCAGCGaa                                                                              <  2:153171/140‑1 (MQ=255)                                                                                                                                                                                                                                            cccTTCTTTGATTCAGGACCCAGTCTGATGAACCATGCACCGCATTTATATTTCGCCTGGCAACAACTCGTCGAAAAAAGCCAGCTCATGTTACGCCTGGCAACGGAAGAACAATGGGACGAACTCATCGCCAGCGAAAt                                                                            >  2:139023/1‑140 (MQ=255)                                                                                                                                                                                                                                                tcttTGATTCAGGACCCAGTCTGATGAACCATGCACCGCATTTATATTTCGCCTGGCAACAACTCGTCGAAAAAAGCCAGCTCATGTTACGCCTGGCAACGGAAGAACAATGGGACGAACTCATCGCCAGCGAAATGGCg                                                                        <  1:139025/140‑1 (MQ=255)                                                                                                                                                                                                                                                            gACCCAGTCTGATGAACCATGCACCGCATTTATAtt                                                                                                                                                                    >  2:392767/1‑36 (MQ=255)                                                                                                                                                                                                                                                              |                                                                                                                                                                                                    ATCAGCAAGGCAAAGGCGTCTCTTTGTCAAAAGCGATCAACATCATTGAGAACGGACTGCGGGTGAGTCTTGATGAAGAGAGCAAAGACGAACTAACCCAAAACTTGATTGCTCTTTATAGCTATATGGTCAGGCGCTTGCTGCAAGCCAATTTACGCAACGATGTCTCCGCAGTCGAAGAAGTGGAAGCATTAATGCGCAATATTGCCGATGCCTGGAAAGAGTCGTTACTCTCCCCTTCTTTGATTCAGGACCCAGTCTGATGAACCATGCACCGCATTTATATTTCGCCTGGCAACAACTCGTCGAAAAAAGCCAGCTCATGTTACGCCTGGCAACGGAAGAACAATGGGACGAACTCATCGCCAGCGAAATGGCGTATGTGAATGCGGTGCAGGAGATTGCACATTTGACTGAAGAGGTTGACCCGTCCACCACGATGCAGGAGC  >  CP009273/1998932‑1999380

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑