Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,023,559	A→G	T223A (ACT→GCT)	fliR →	flagellar biosynthesis protein FliR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,023,559	0	A	G	92.0%	76.4 / ‑0.7	25	T223A (ACT→GCT)	fliR	flagellar biosynthesis protein FliR
Reads supporting (aligned to +/- strand):  ref base A (0/2);  new base G (7/16);  total (7/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.69e-01

AACGGTCATTTATGGTTGATTTCACTGCTGGTCGATACCTTTCACACCCTGCCGATTGGTGGCGAACCGTTGAACAGCAATGCGTTTCTGGCACTCACCAAAGCAGGGAGTTTGATTTTCCTTAACGGGCTGATGCTGGCGTTACCGCTCATTACTCTGCTGCTGACACTGAATCTGGCATTAGGTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGACTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACT  >  NC_000913/2023313‑2023801                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                   aaCGGTCATTTATGGTTGATTTCACTGCTGGTCGATACCTTTCACTCCCTGCCGATTGGTGGCGAACCGTTGAACAGCAATGCGTTTCTGGCACTCGCCAAAGCAGGGAGTTTGATTTTCCTTAACGGGCTGATGCTGGCGTTACCGCTCATTACTCTGCTGCTGACACTGAATCTGGCATTAGGTTTACTTAATCGTATGTCCCCGCAATTATCCATTTTTGTTATTTGATTTCCATTAACTCTGGCTg                                                                                                                                                                                                                                                 <  2:95190/250‑1 (MQ=255) aaCGGTCATTTATGGTTGATTTCACTGCTGGTCGATACCTTTCACACCCTGCCGATTGGTGGCGAACCGTTGAACAGCAATGCGTTTCTGGCACTCACCAAAGCAGGGAGTTTGATTTTCCTTAACGGGCTGATGCTGGCGTTACCGCTCATTACTCTGCTGCTGACACTGAATCTGGCATTAGGTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGt                                                                                                                                                                                                                                                <  1:55962/251‑1 (MQ=255)   cGGTCATTTATGGTTGATTTCACTGCTGGTCGATACCTTTCACACCCTGCCGATTGGTGGCGAACCGTTGAACAGCAATGCGTTTCTGGCACTCACCAAAGCAGGGAGTTTGATTTTCCTTAACGGGCTGATGCTGGCGTTACCGCTCATTACTCTGCTGCTGACACTGAATCTGGCATTAGGTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGTCg                                                                                                                                                                                                                                              >  1:477862/1‑251 (MQ=255)    ggTCATTTATGGTTGATTTCACTGCTGGTCGATACCTTTCACACCCTGCCGATTGGTGGCGAACCGTTGAACAGCAATGCGTTTCTGGCACTCACCAAAGCAGGGAGTTTGATTTTCCTTAACGGGCTGATGCTGGCGTTACCGCTCATTACTCTGCTGCTGACACTGAATCTGGCATTAGGTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGTCgg                                                                                                                                                                                                                                             <  1:69725/251‑1 (MQ=255)         tttATGGTTGATTTCACTGCTGGTCGATACCTTTCACACCCTGCCGATTGGTGGCGAACCGTTGAACAGCAATGCGTTTCTGGCACTCACCAAAGCAGGGAGTTTGATTTTCCTTAACGGGCTGATGCTGGCGTTACCGCTCATTACTCTGCTGCTGACACTGAATCTGGCATTAGGTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGTCGGCAtct                                                                                                                                                                                                                                        >  1:296658/1‑251 (MQ=255)           tATGGTTGATTTCACTGCTGGTCGATACCTTTCACACCCTGCCGATTGGTGGCGAACCGTTGAACAGCAATGCGTTTCTGGCACTCACCAAAGCAGGGAGTTTGATTTTCCTTAACGGGCTGATGCTGGCGTTACCGCTCATTACTCTGCTGCTGACACTGAATCTGGCATTAGGTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGTCGGCAtctc                                                                                                                                                                                                                                       <  2:477862/250‑1 (MQ=255)                             tgggcGATACCTTTCACACCCTGCCGATTGGTGGCGAACAGTTGAACAGCAATGCGTTTCTGGCACTCACCAAAGCAGGGAGCTTGATTTTCCTTAACGGGCTGATGCTGGCGTTACCGCTCATTACTCTGCTGCTGACACTGAATCTGGCATGAGGTTTACTTAATCGTATGGACCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGTCGGCATCTCTTTAATGGCGGCATTa                                                                                                                                                                                                                       >  2:319190/5‑248 (MQ=255)                                          tCACACCCTGCCGATTGGTGGCGAACCGTTGAACAGCAATGCGTTTCTGGCACTCACCAAAGCAGGGAGTTTGATTTTCCTTAACGGGCTGATGCTGGCGTTACCGCTCATTACTCTGCTGCTGACACTGAATCTGGCATTAGGTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCa                                                                                                                                                                                                        <  1:329743/250‑1 (MQ=255)                                            atacCCTGACGATTGGTGGCGAACCGTTGAACAGCAATGCGTTTCTGGCACTCACCAAAGCAGGGAGTTTGATTTTCCTTAACGGGCTGATGCTGGCGTTACCGTTCATTACTCTGCTGCTGACACTGAATCTGGCATTAGGTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGAACCt                                                                                                                                                                                                     <  2:209387/249‑1 (MQ=255)                                              ccccTGCCGATTGGTTGCGAACCGTTGAACAGCAATGCGTTTCTGGCACTCACCAAAGCAGGGAGTTTGATTTTCCTTAACGGGCTGATGCTGGCGTTACCGCTCATTACTCTGCTGCTGACACCGAATCTGGCATTAGGTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCttt                                                                                                                                                                                                   <  2:485214/250‑1 (MQ=255)                                              acCCTGCCGATTGGTGGCGAACCGTTGAACAGCAATGCGTTTCTGGCACTCACCAAAGCAGGGAGTTTGATTGTCCTTAACGGGCTGATGCTGGCGTTACCGCTCATTACTCTGCTGCTGACACTGAATCTGGCATTAGGTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCttt                                                                                                                                                                                                   <  1:456123/251‑1 (MQ=255)                                                     cGATTGGTGGCGAACCGTTGAACAGCAATGCGTTTCTGGCACTCACCAAAGCAGGGAGTTTGATTTTCCTTAACGGGCTGATGCTGGCGTTACCGCTCATTACTCTGCTGCTGACACTGAATCTGGCATTAGGTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGaa                                                                                                                                                                                            <  1:241346/251‑1 (MQ=255)                                                                                                                             aCGGGCTGATGCTGGCGTTACCGCTCATTACTCTGCTGCTGACACTGAATCTGGCATTAGGTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAAc                                                                                                                    <  1:438199/251‑1 (MQ=255)                                                                                                                                        cTGGCGTTACCGCTCATTACTCTGCTGCTGACACTGAATCTGGCATTAGGTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTTCGTAACGTTTATCATGt                                                                                                         >  1:79363/1‑251 (MQ=255)                                                                                                                                                aCCGCTCATTACTCTGCTGCTGACACTGAATCTGGCATTAGGTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGACTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTa                                                                                                  <  1:40787/250‑1 (MQ=255)                                                                                                                                                      cATTACTCTGCTGCTGACACGGAATCTGGCATTAGGTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTTCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGAtt                                                                                            <  2:281228/250‑1 (MQ=255)                                                                                                                                                       aTTACTCTGCTGCTGACACTGAATCTGGCATTAGGTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTAt                                                                                          <  1:232290/251‑1 (MQ=255)                                                                                                                                                                               cTGGCATTAGGTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACAt                                                                  >  2:56843/1‑251 (MQ=255)                                                                                                                                                                                        ggTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATCGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAgg                                                          >  1:425805/1‑250 (MQ=255)                                                                                                                                                                                         gTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGTCTGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGATCATCTTCCAGGAt                                                        <  2:144586/251‑1 (MQ=255)                                                                                                                                                                                             aattactCGTATGGCCCCGCAATTATCCATTTTTGTGAGTGGATTTCCAATAACTCTGGCTGTCGGCATCTCTTTAATGTCGGCATTAATGCCGTTACTTGCACCTTAGTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATAGTATTAGTGAGTTTACATGAATATAATTCCGTAACGTTTATCATGTTATCCTAGCGGGTATCCAAAAAAAAATTCCTACGAACATTTTCCAGGAGACTc                                                    <  2:333845/245‑1 (MQ=255)                                                                                                                                                                                                                    tATCCATTTTTGTTATTGGATTTCCATTAACTCTGGCTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTa                              <  1:467493/250‑1 (MQ=255)                                                                                                                                                                                                                            tttGTTATTGGATTTCCATTAACTCTGACTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCATGATACTCCTGCAGCGAAATATTTGTTTTAAGctcact                      <  1:373040/250‑1 (MQ=255)                                                                                                                                                                                                                                       aTTTCCATTAACTCTGGCTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCaa          <  2:296658/251‑1 (MQ=255)                                                                                                                                                                                                                                               tAACTCTGGCTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttact  >  1:130970/1‑251 (MQ=255)                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                   AACGGTCATTTATGGTTGATTTCACTGCTGGTCGATACCTTTCACACCCTGCCGATTGGTGGCGAACCGTTGAACAGCAATGCGTTTCTGGCACTCACCAAAGCAGGGAGTTTGATTTTCCTTAACGGGCTGATGCTGGCGTTACCGCTCATTACTCTGCTGCTGACACTGAATCTGGCATTAGGTTTACTTAATCGTATGGCCCCGCAATTATCCATTTTTGTTATTGGATTTCCATTAACTCTGACTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACT  >  NC_000913/2023313‑2023801

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑