Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,014,421	A→G	N398S (AAC→AGC)	fliF →	flagellar basal‑body MS‑ring and collar protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,014,421	0	A	G	82.3%	37.6 / ‑2.4	17	N398S (AAC→AGC)	fliF	flagellar basal‑body MS‑ring and collar protein
Reads supporting (aligned to +/- strand):  ref base A (2/1);  new base G (11/3);  total (13/4)
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

GCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACAAAACCTTGCCAGATGGCAAACCGTTGCCTCTCAGCAACGAACAGATGAAGCAAATTGAAGATCTGACCCGCGAGGCGATGGGCTTTTCTGAAAAACGCGGTGACTCGCTCAATGTCGTTAACTCGCCGTTCAATAGCAGTGACGAAAGCGGCGGAGAACTGCCATTCTGGCAACAGCAAGCGTTTATCGATCAGTTACTTGCTGCCGGTCGCTGGTTGCTGGTACTGCTGGTGGCGTGGCTG  >  NC_000913/2014232‑2014626                                                                                                                                                                                              |                                                                                                                                                                                                              nccAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGCAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACAAAACCTTGTCAGATGGCAAACCGTTGCCTCTCAGCAGCGAACAGATGAAGCAAATTGAAGATCTGAACCGCGAGGCGATGGGCTTTTCTGaaaaaagc                                                                                                                                                  >  1:29277/2‑248 (MQ=255)                                tGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATAGCACCATTCGTCATACCAAAATGAACGTGGGCGATCTGCACCCTCTATCAGTCGCCGTCGTGGTGAATTACAAACACTTGCCAGATGGCAAACCGTTGCCTCTCAGCCGCGAACAGATGAAGCAAATTGAAGATCTGACCCGCGAGGCGATGGGCTTTTCTGAAAAACGCGGTGACTCGCTCAATGTCGTTAACTCGCCGt                                                                                                                   >  1:145428/1‑251 (MQ=255)                                                                      ncGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACAAAACCTTGCCAGATGGCAAACCGTTGCCTCTCAGCAGCGAACAGATGAAGCAAATTGGAGATCTGACCCGCGAGGCGATGGGCTTTTCTGAAAAACGCGGTGACTCGCTCAATGTCGTTAACTCGCCGTTCAATAGCAGTGACGAAAgc                                                                                               >  1:81091/2‑233 (MQ=255)                                                                                     ccATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACAAAACCTTGCCAGATGGCAAACCGTTGCCTCTCAGCAGCGAACAGATGAAGCAAATTGAAGATCTGACCCGCGAGGCGATGGGCTTTTCTGAAAAACGCGGTGACTCGCTCAATGTCGTTAACTCGCCGTTCAATAGCAGTGACGAAAGCGGCGGAGAACTGCCATTCTGGCa                                                                        >  1:109561/1‑241 (MQ=255)                                                                                       aTTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACAAAACCTTGCCAGATGGCAAACCGTTGCCTCTCAGCAGCGAACAGATGAAGCAAATTGAAGATCTGACCCGCGAGGCGATGGGc                                                                                                                                                                 <  1:10801/150‑1 (MQ=255)                                                                                                    aaaTGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACAAAACCTTGCCAGATGGCAAACCGTTGCCTCTCAGCAGCGAACAGATGAAGCAAATTGAAGATCTGACCCGCGAggn                                                                                                                                                                        <  1:199140/130‑2 (MQ=255)                                                                                                    aaaTGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACAAAACCTTGCCAGATGGCAAACCGTTGCCTCTCAGCAGCGAACAGATGAAGCAAATTGAAGATCTGACCCGCGAGGc                                                                                                                                                                        >  2:199140/1‑130 (MQ=255)                                                                                                            ntGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGCATTACAAAACCTTGCCAGATGGCAAACCGTTGCCTCTCAGCAGCGAACAg                                                                                                                                                                                                        >  1:31001/2‑90 (MQ=255)                                                                                                                                        cgGTCGTGGGGAATTACAAAACCTTGCCAGAAGGCAAACCGATGCCTCTAAGCCGGGAACAGATGAAACAAATTGAAGATCTGACCCGCGAGGCGATGGGCTTTTCTGAAAAACGCGGTGACTCGCTCAATGTCGTTAACTCGCCGTTCAATAGCAGTGACGAAAGCGGCGGAGAACTGCCATTCTGGCAACAGCAAGCGTTTATCGATCAGtt                                                >  1:286624/1‑214 (MQ=255)                                                                                                                                          gTCGTGGTGAATTACAAAACCTTGCCAGATGGCAAACCGTTGCCTCTCAGCAGCGAACAGATGAAGCAAATTGAAGATCTGACCCGCGAGGCGATGGGCTTTTCTGAAAAACGCGGTGACTCGCTCAATGTCGTTAACTCGCCGTTCAATAGCAGTGACGAAAGCGGCGGAGAACTGCCATTCTTGCAACAGCAAGCGTTTATCGATCAGTTGCTGGCTGCCGGTCGCTGGTTGCTGGTan                   <  1:78415/241‑2 (MQ=255)                                                                                                                                            cGTGGTGAATTACAAAACCTTGCCAGATGGCAAACCGTTGCCTCTCAGCAAAGAACAGATGAAGCAAGTTGACGATCTGACCAGCGAGGCGATGGGCTTTTCTGAAAAACGCGGTGACTCGCTCAATGTCg                                                                                                                               >  1:231328/1‑131 (MQ=255)                                                                                                                                              tggtgAATTACAAAACCTTGCCAGATGGCAAACCGTTGCCTCTCAGCAGCGAACAGATGCAGCAAATTGAAGAACTGACCAGCGAGGCGATGGGCTTTTCTGaaaa                                                                                                                                                      >  1:326020/1‑106 (MQ=255)                                                                                                                                                 tgAATTACAAAACCTTGCCAGATGGCAAACCGTTGCCATTCAGCAGCGCAAAGATGCAGCAAATTGAAGCTCTGACACGCGAGGCGATGGGCTTTTCTGAAAAACGAGGTGACTCGCTCAATGTCGGTAACTCGCCGTTCAATAGCAGTGACGAAAGCGGCGGAGAACTGACATTCTGGCAACAGCAAGCGTTTATCGATCAGTTACTTGCTGACGGTCGCTGGTTGCTGGTACTGCTGGTGGCGGGgctg  >  1:144695/1‑251 (MQ=255)                                                                                                                                                                         gCAAACCGTTGCCTCTCAGCAACGAACAGATGAAGCAAATTGAAGATCTGAcc                                                                                                                                                                                >  1:75986/1‑53 (MQ=255)                                                                                                                                                                         gCAAACCGTTGCCTCNCANNAACGAANAGATGAAGCAAATTGAAGATCTGAcc                                                                                                                                                                                <  2:75986/53‑1 (MQ=255)                                                                                                                                                                                    ccTCTCAGCAGCGAACAGATGAAGCAAATTGAAGATCTGACCCGCGCGGCGATGGGCTTTTCTGAAACACGCGGTGACt                                                                                                                                           >  1:184842/1‑79 (MQ=255)                                                                                                                                                                                     ctctCAGCAGCGAACAGATGAAGCAAATTGAAGATCTGACCCGCGAGGCGATGGGCTTTTCTGAAAAAcgcg                                                                                                                                                 >  1:138615/1‑72 (MQ=255)                                                                                                                                                                                              |                                                                                                                                                                                                              GCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACAAAACCTTGCCAGATGGCAAACCGTTGCCTCTCAGCAACGAACAGATGAAGCAAATTGAAGATCTGACCCGCGAGGCGATGGGCTTTTCTGAAAAACGCGGTGACTCGCTCAATGTCGTTAACTCGCCGTTCAATAGCAGTGACGAAAGCGGCGGAGAACTGCCATTCTGGCAACAGCAAGCGTTTATCGATCAGTTACTTGCTGCCGGTCGCTGGTTGCTGGTACTGCTGGTGGCGTGGCTG  >  NC_000913/2014232‑2014626

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑