Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,003,470	G→C	A46G (GCG→GGG)	fliC ←	flagellar filament structural protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,003,470	0	G	C	96.2%	72.0 / ‑7.0	26	A46G (GCG→GGG)	fliC	flagellar filament structural protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base C (16/9);  minor base T (0/1);  total (16/10)
Fisher's exact test for biased strand distribution p-value = 3.85e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACCAGATACGCGGTCAATTTCATCCAGACGGGATTTAATTTCGTCCTGGATAGAAGACAGATCAGACTCAGAGTTAGTACCGGTAGTGGCCTGTACCGTCAGTTCACGCACACGCTGTAAGTTGTTGTTGATTTCGGACAGCGCGCCTTCGGTGGTCTGCGCAACGGAGATACCGTCGTTGGCGTTACGGGCCGCCTGAGTCAGGCCTTTAATGTTAGAGGTGAAACGGTTAGCAATCGCCTGACCCGCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGACAGCGCAGACTGGTTCTTGTTGATATTATTTTGAGTGATCAGCGAGAGGCTGTTGGTATTAATGACTTGTGCCATGATTCGTTATCCTATATTGCAAGTCGTTGATTACGTATTGGGTTTCCACCCGTCGGCTCAATCGCCGTCAACCCTGTTATCGTCTGTCGTAAAACAACCTTTAGAAT  >  NC_000913/2003223‑2003713                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                    aCCAGATACGCGGTCAATTTCATCCAGACGGGATTTAATTTCGTCCTGGATAGCAGACAGATCAGACTCAGAGTTAGTACCGGTAGTGGCCTGTACCGTCAGTTCACGCACACGCTGTAAGTTGTTGTTGATTTCGGACAGCGCGCCTTCGGTGGTCTGCGCAACGGAGATACCGTCGTTGGAGTTACGGGCCGCCTGAGTCAGGCCTTTAATGTTAGAGGTGAAACGGTTAGCAATCGACTGACCCCCTg                                                                                                                                                                                                                                                  >  1:293077/1‑251 (MQ=255)                            aCGGGATTTAATTTCGTCCTGGATAGCAGACAGATCAGACTCAGAGTTAGTACCGGTAGTGGCCTGTACCGTCAGTTCACGCACACGCTGTAAGTTGTTGTTGATTTCGGACAGCGCGCCTTCGGTGGTCTGCGCAACGGAGATACCGTCGTTGGCGTTACGGGCCGCCTGAGTCAGGCCTTTAATGTTAGAGGTGAAACGGTTAGCAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGc                                                                                                                                                                                                                        >  1:85592/1‑250 (MQ=255)                                                               cAGACTCAGAGTTAGTACCGGTAGTGGCCTGTACCGTCAGTTCACGCACACGCTGTAAGTTGTTGTTGATTTCGGACAGCGCGCCTTCGGTGGTCTGCGCAACGGAGATACCGTCGTTGGCGTTACGGGCCGCCTGAGTCAGGCCTTTAATGTTAGAGGTGAAACGGTTAGCAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGACAgc                                                                                                                                                                                    <  1:238304/251‑1 (MQ=255)                                                                 gACTCAGAGTTAGTACCGGTAGTGGCCTGTACCGTCAGTTCACGCACACGCTGTAAGTTGTTGTTGATTTCGGACAGCGCGCCTTCGGTGGTCTGCGCAACGGAGATACCGTCGTTGGCGTTACGGGCCGCCTGAGTCAGGCCTTTAATGTTAGAGGTGAAACGGTTAGCAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGACAgcgc                                                                                                                                                                                  >  1:83659/1‑251 (MQ=255)                                                                              taacGGTAGTGGCCTGTACCGTCAGTTCACGCACACGCTGTAAGTTGTTGTTGATTTCGGGCAGCGCGCCTTCGGTGGTCTGCGCGACGGAGATACCGTCGTTGGCGTTACGGGCCGCTTGAGTCAGGCCTTTCATGTTAGAGTTGAAACGGTTAGCAATCGACTGAACCCCTGCTTCATCCTTCGAGATGTTCATACGCCAACCAGAAGACAGACGCTCGATATGACTCGCGAGCGAAGACTGGTTCttt                                                                                                                                                                     >  2:141299/4‑250 (MQ=255)                                                                                        gtccTGTACCGTCAGTTCACGCACTCGCTGTAAGTTGTGGGTGATTTCGGCCAGCGCGCCTGCGGTGGTCTGCGCAACGGAGATACCGTCGTTGGCGTTACGGGCCGCCTGAGTCAGGCCTTTAATGTTAGAGGTGAAACGGTTAGCAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGACAGCGCAGACTGGTTCTTGTTGAtattat                                                                                                                                                           <  2:138551/249‑1 (MQ=255)                                                                                         gCCTGTACCGTCAGTTCACGCACACGCTGTAAGTTGTTGTTGATTTCGGACAGCGCGCCTTCGGTGGTCTGCGCAACGGAGATACCGTCGTTGGCGTTACGGGCCGCCTGAGTCAGGCCTTTAATGTTAGAGGTGAAACGGTTAGCAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGACAGCGCAGACTGGTTCTTGTTGATattatt                                                                                                                                                          >  1:271897/1‑251 (MQ=255)                                                                                          ccTGTACCGTCAGTTCACGCACACGCTGTAAGTTGTTGTTGATTTCGGACAGCGCGCCTTCGGTGGTCTGCGCAACGGAGATACCGTCGTTGGCGTTACGGGCCGCCTGAGTCAGGCCTTTAATGTTAGAGGTGAAACGGTTAGCAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGACAGCGCAGACTGGTTCTTGTTGATATTAttt                                                                                                                                                         >  1:389916/1‑251 (MQ=255)                                                                                                 cGTCAGTTCACGCACACGCTGTAAGTTGTTTTTGATTTCGGACAGCGCGCCTGCGGTGGTCTTCGCAACGGAGATTCCTTCGTTGGCGTTACGGGCCGCCTGAGTCAGGCCTTTAATGTTAGATGTGAAACGGTTAGCAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGTCAGACGCTCGATAGAACTCGACAGCGCAGACTGGTTCTTGTTGATATTATTTTGAGTGa                                                                                                                                                  <  1:50959/251‑1 (MQ=255)                                                                                                  ggcAGTTCACGCACACGCTGTAAGTTGTTGGTGATTTCGGACAGCGCGCCTTCGGTGGTCTGCGCAACGGAGATACCGTCGTTGGCGTTACGGGCCGCCTGAGTCAGGCCTTTAATGTTAGAGGTGAAACGGTTAGCAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGACAGCGCAGACTGGTTCTTGTTGATATTATTTTGAGTGAt                                                                                                                                                 <  2:197395/249‑1 (MQ=255)                                                                                                         cACGCACACGCTGTAAGTTGTTGTTGATTTCGGACAGCGCGCCTTCGGTGGTCTGCGCAACGGAGATACCGTCGTTGGCGTTACGGGCCGCCTGAGTCAGGCCTTTAATGTTAGAGGTGAAACGGTTAGCAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGACAGCGCAGACTGGTTCTTGTTGATATTATTTTGAGTGATCAGCg                                                                                                                                            >  1:166957/1‑249 (MQ=255)                                                                                                            gCACATGCTGTAAGTTGTTGTGGATTTCGGGCAGCGCGCCTTCGGTGGGCTGCGCAACGGAGATACCGTCGTTGGCGTTACGGGCCGCCTGAGTCAGGCCTTTAATGTTAGAGGTGAAACGGTTAGCAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGACAGCGCAGACTGGTTCTTGTTGATATTATTTTGAGTGATCAGCGagagt                                                                                                                                       <  2:271897/251‑2 (MQ=255)                                                                                                                          ttgttgttgATTTCGGACAGCGCGCCTTCGGTGGTCTGCGCAACGGAGATACCGTCGTTGGCGTTACGGGCCGCCTGAGTCAGGCCTTTAATGTTAGAGGTGAAACGGTTAGCAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGACAGCGCAGACTGGTTCTTGTTGATATTCTTTTGAGGGATCAGCGAGAGGCTGTTGGTATTAAt                                                                                                                         >  2:464448/1‑251 (MQ=255)                                                                                                                            gttgttgATTTCGGACAGCGCGCCTTCGGTGGTCTGCGCAACGGAGCTACCGTCGTTGGCGTTACGGGCCGCCTGAGTCAGGCCTTTAATGTTAGAGGTGAAACGGCTCGCAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGCCAGCGCAGACTGGTTCTTGTTGATATTATTTTGGGTGCTCATCGGGAGGCTTGTGGTATTAATg                                                                                                                        >  2:143790/1‑250 (MQ=255)                                                                                                                                                           gtCTGCGCAACGGTGAGAGCGATGTTGGCGTGTCGGGCCGCCTGATTCAGTCCTTGATTGTTAGAGGGGAAACGGTTAGCAATCGACTGACCCCCTGCGTCATCATACGCGCTGTGAATACGCAAGCCAGAAGAAAGACGTTCGATAGAACGCGACAGCGCAGACTGGTTCTTGTTGATATTATTTTGAGTGATCAGCGAGCTGCTGTTGGTATTAATGACTTTTGCCATGATTCGTTATCCGATATTGct                                                                                        <  2:391988/251‑2 (MQ=255)                                                                                                                                                                 gcAACGGAGATACCGTCGTTGGCGTTACGGGCCGCCTGAGTCAGGCCTTTAATGTTAGAGGTGAAACGGTTAGCAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGACAGCGCAGACTGGTTCTTGTTGATATTATTTTGAGTGATCAGCGAGAGGCTGTTGGTATTAATGACTTGTGCCATGATTCGTTATCCTATATTGCAAGTCGt                                                                                  <  1:20083/251‑1 (MQ=255)                                                                                                                                                                                 cgtTGGCGTTACGGGCCGCCTGAGTCAGGCCTTTAATGTTAGAGGTGAAACGGTTAGCAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGACAGCGCAGACTGGTTCTTGTTGATATTATTTTGAGTGATCAGCGAGAGGCTGTTGGTATTAATGACTTGTGCCATGATTCGTTATCCTATATTGCAAGTCGTTGATTACGTATTGGGt                                                                  <  1:307862/251‑1 (MQ=255)                                                                                                                                                                                                             gCCTTTAATGTGAGAGGTGTAACGTGTAGCAAGCGACTGACCCCCTGCGTCATCCTGCGCGCTGTTAATACGCAAGTCAGAAGACAGACGCTTGATGGAACTCGACAGCGGAGATTGGTTCTGGTTGATATTATTTTGAGTGATCAGCGAGAGGCTGTTGGTATTAATGGCTTGTGCCATTAGTCGTTATCCTATATTGTAAGTCGTTGATTAGGTATTGGGTTTCCACCCGTCGGCTCAATCGGCGTCaa                                      <  2:443422/251‑1 (MQ=255)                                                                                                                                                                                                                    aTGTTAGAGGTGAAACGGTTAGCAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGACAGCGCAGACTGGTTCTTGTTGATATTATTTTGAGTGATCAGCGAGAGGCTGTTGGTATTAATGACTTGTGCCATGATTCGTTATCCTATATTGCAAGTCGTTGATTACGTATTGGGTTTCCACCCGTCGGCTCAATCGCCGTCAACCCTGtt                               >  1:281556/1‑251 (MQ=255)                                                                                                                                                                                                                         agagGGGAAACGGTTAGCAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGACAGCGCAGACTGGTTCTTGTTGATATTATTTTGAGTGATCAGCGAGAGGCTGTTGGTATTAATGACTTGTGCCATGATTCGTTATCCTATATTGCAAGTCGTTGATTACGTATTGGGTTTCCACCCGTCGGCTCAATCGCCGTCAACCCTGTTATcat                          >  1:192512/1‑249 (MQ=255)                                                                                                                                                                                                                            ggTGAAACGGTTAGCAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGACAGCGCAGACTGGTTCTTGTTGATATTATTTTGAGTGATCAGCGAGAGGCTGTTGGTATTAATGACTTGTGCCATGATTCGTTATCCTATATTGCAAGTCGTTGATTACGTATTGGGTTTCCACCCGTCGGCTCAATCGCCGTCAACCCTGTTATCGTCTg                       >  1:189458/1‑251 (MQ=255)                                                                                                                                                                                                                               gAAACGGTTAGCAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGACAGCGCAGACTGGTTCTTGTTGATATTATTTTGAGTGATCAGCGAGAGGCTGTTGGTATTAATGACTTGTGCCATGATTCGTTATCCTATATTGCAAGTCGTTGATTACGTATTGGGTTTCCACCCGTCGGCTCAATCGCCGTCAACCCTGTTATCGTCTGTCg                    >  1:383318/1‑251 (MQ=255)                                                                                                                                                                                                                                          cAATCGACTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGACAGCGCAGACTGGTTCTTGTTGATATTATTTTGAGTGATCAGCGAGAGGCTGTTGGTATTAATGACTTGTGCCATGATTCGTTATCCTGTATTGCAAGTCGTTGATTACGTATTGGGTTTCCACCCGTCGGCTCAATCGCCGTCAACCCTGTTATCGTCTGTCGTAAAACAACCt         >  1:276672/1‑251 (MQ=255)                                                                                                                                                                                                                                          cAATCGACAGACCCCCTGCGTCATCCTTCTCGCTGTTAATACGCAAGCCAGAAGCCAGACGCTCGATAGAACTCGACAGCGCTGACTGGTTCTTGTTGATATTATTTTGAGTGATCAGCGAGAGGCTGGTGGTATTAATGACTTTTGCCATGATTCGTTATCCTATATTGCAAGTCGGTGATTACATATTGGGTTTCCACCCGTCGGCCCAATCGCCCTCAACCCTGTTATCGTCTGTCGTAAAACAACCt         >  2:236423/1‑251 (MQ=255)                                                                                                                                                                                                                                           aaacgacTGACCCTCTGCGTCATCCTGCGCCCTGTGAATACGCAAGCCAGAAGACTGACGCTCGATAGAACTCGACAGCGCAGACTTGTTCTTGTTGATATTAGTTTGTGTAATCAGCGAGAGGCTGTTGGTATTAATGACTTGTTCCATGATTCGTTATCCTATATTGCAAGTCGTTGATTACGTATTGGGTTTCCACCCGTCGGCTCAATCGCCGTCAACCCTGTTATCGTCTGTCGTAAAACAACCtt        <  2:94176/245‑1 (MQ=255)                                                                                                                                                                                                                                                 cTGACCCCCTGCGTCATCCTTCGCGCTGTTAATACGCAAACCAGAAGACAGACGCTCGATAGAACTCGACAGCGCAGACTGGTTCTTGTTGATATTATTTTGAGTGATCAGCGAGAGGATGTTGGTATTAATGACTTGTGCCATGATTCGTTATCCTATATTGCAAGTCGTTGATTACGTATTGGGTTTCCACCCGTCGGCTCACTCGCCGTCAACCCTGCTATCGTCTGTCGTAAAACAACCTTTAGAAt  >  1:353134/1‑251 (MQ=255)                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                    ACCAGATACGCGGTCAATTTCATCCAGACGGGATTTAATTTCGTCCTGGATAGAAGACAGATCAGACTCAGAGTTAGTACCGGTAGTGGCCTGTACCGTCAGTTCACGCACACGCTGTAAGTTGTTGTTGATTTCGGACAGCGCGCCTTCGGTGGTCTGCGCAACGGAGATACCGTCGTTGGCGTTACGGGCCGCCTGAGTCAGGCCTTTAATGTTAGAGGTGAAACGGTTAGCAATCGCCTGACCCGCTGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACGCTCGATAGAACTCGACAGCGCAGACTGGTTCTTGTTGATATTATTTTGAGTGATCAGCGAGAGGCTGTTGGTATTAATGACTTGTGCCATGATTCGTTATCCTATATTGCAAGTCGTTGATTACGTATTGGGTTTCCACCCGTCGGCTCAATCGCCGTCAACCCTGTTATCGTCTGTCGTAAAACAACCTTTAGAAT  >  NC_000913/2003223‑2003713

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑