Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,546,272	A→C	T393P (ACC→CCC)	fimD →	type I fimbriae usher protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,546,272	0	A	C	96.0%	65.0 / NA	25	T393P (ACC→CCC)	fimD	type I fimbriae usher protein
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base C (8/16);  total (9/16)
Fisher's exact test for biased strand distribution p-value = 3.60e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATGACATTTATAATAGTACGGTGCCACCGGGGCCTTTTACCATCAACGATATCTATGCCGCAGGTAATAGTGGTGACTTGCAGGTAACGATCAAAGAGGCTGACGGCAGCACGCAGATTTTTACCGTACCCTATTCGTCAGTCCCGCTTTTGCAACGTGAAGGGCATACTCGTTATTCCATTACGGCAGGAGAATACCGTAGTGGAAATGCGCAGCAGGAAAAAACCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCGGCTGGCTGGACAATATATGGTGGAACGCAACTGGCGGATCGTTATCGTGCTTTTAATTTCGGTATCGGGAAAAACATGGGGGCACTGGGCGCTCTGTCTGTGGATATGACGCAGGCTAATTCCACACTTCCCGATGACAGTCAGCATGACGGACAATCGGTGCGTTTTCTCTATAACAAATCGCTCAATGAATCAGGCACGAATATT  >  NC_000913/4546048‑4546517                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                      aTGACATTTATACTAGTACGGTGCCACCGGGGCCTTTTACCATCAACGATATCTATGCCGCAGGTAATAGTGGTGACTTGCAGGTAACGATCAAAGAGGCTGACGGCAGCACGCAGATTTTTACCGTACCCTATTCGTCAGTCCCGCTTTTGCAACGTGAAGGGCATACTCGTTATTCCATTACGGCAGGAGACTCCCGTAGTGGAAATGCGCCGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACTc                                                                                                                                                                                                                             >  1:27645/1‑251 (MQ=255)  ggACATTTATAATAGTACGGTGCCACCGGGGCCTTTTACCATCAACGATATCTATGCCGCAGGTAATAGTGGTGACTTGCAGGTAACGATCAAAGAGGCTGACGGCAGCACGCAGATTTTTACCGTACCCTATTCGTCAGTCCCGCTTTTGCAACGTGAAGGGCATACTCGTTATTCCATTACGGCAGGAGAATACCGTAGTGGAAATGCGCAGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACTcc                                                                                                                                                                                                                            <  1:127326/250‑1 (MQ=255)          ataataGTACGGTGCCACCGGGGCCTTTTACCATCAACGATATCTATGCCGCAGGTAATAGTGGTGACTTGCAGGTAACGATCAAAGAGGCTGACGGCAGCACGCAGATTTTTACCGTACCCTATTCGTCAGTCCCGCTTTTGCAACGTGAAGGGCATACTCGTTATTCCATTACGGCAGGAGAATACCGTAGTGGAAATGCGCAGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACTCCACGGCCtt                                                                                                                                                                                                                    <  1:265977/251‑1 (MQ=255)            aataGTACGGTGCCACCGGGGCCTTTTACCATCAACGATATCTATGCCGCAGGTAATAGTGGTGACTTGCAGGTAACGATCAAAGAGGCTGACGGCAGCACGCAGATTTTTACCGTACCCTATTCGTCAGTCCCGCTTTTGCAACGTGAAGGGCATACTCGTTATTCCATTACGGCAGGAGAATACCGTAGTGGAAATGCGCAGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTcc                                                                                                                                                                                                                  <  1:31197/251‑1 (MQ=255)                    ggTGCCACCGGGGCCTTTTACCATCAACGATATCTATGCCGCAGGTAATAGTGGTGACTTGCAGGTAACGATCAAAGAGGCTGACGGCAGCACGCAGATTTTTACCGTACCCTATTCGTCAGTCCCGCTTTTGCAACGTGAAGGGCATACTCGTTATTCCATTACGGCAGGAGAATACCGTAGTGGAAATGCGCAGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCggctggct                                                                                                                                                                                                          <  1:124175/251‑1 (MQ=255)                    ggTGCCACCGGGGCCTTTTACCATCAACGATATCTATGCCGCAGGTAATAGTGGTGACTTGCAGGTAACGATCAAAGAGGCTGACGGCAGCACGCAGATTTTTACCGTACCCTATTCGTCAGTCCCGCTTTTGCAACGTGAAGGGCATACTCGTTATTCCATTACGGCAGGAGAATACCGTAGTGGAAATGCGCAGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCggctggct                                                                                                                                                                                                          <  1:206238/251‑1 (MQ=255)                                    tttACCATCAACGATATCTATGCCGCAGGTAATAGTGGTGACTTGCAGGTAACGATCAAAGAGGCTGACGGCAGCACGCAGATTTTTACCGTACCCTATTCGTCAGTCCCGCTTTTGCAACGTGAAGGGCATACTCGTTATTCCATTACGGCAGGAGAATACCGTAGTGGAAATGCGCAGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCGGCTGGCTGGACAATATAtggtgg                                                                                                                                                                                          >  1:198829/1‑251 (MQ=255)                                    tttACCATCAACGATATCTATGCCGCAGGTAATAGTGGTGACTTGCAGGTAACGATCAAAGAGGCTGACGGCAGCACGCAGATTTTTACCGTACCCTATTCGTCAGTCCCGCTTTTGCAACGTGAAGGGCATACTCGTTATTCCATTACGGCAGGAGAATACCGTAGTGGAAATGCGCAGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCGGCTGGCTGGACAATATAtggggg                                                                                                                                                                                          >  1:258012/1‑248 (MQ=255)                                                  tatCTATGCCGCAGGTAATAGTGGTGACTTGCAGGTAACGATCAAAGAGGCTGACGGCAGCACGCAGATTTTTACCGTACCCTATTCGTCAGTCCCGCTTTTGCAACGTGAAGGGCATACTCGTTATTCCATTACGGCAGGAGAATACCGTAGTGGAAATGCGCAGCAGGAAAAAACCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCGGCTGGCTGGACAATATATGGTGGAAAGCAACTGGCgg                                                                                                                                                                            >  1:371167/1‑251 (MQ=255)                                                         gCCGCAGGTAATAGTGGTGACTTGCAGGTAACGATCAAAGGGGCTGACGGCAGCACGCAGATTTTTACCGTACCCTATTCGTCAGTCCCGCTTTTGCAACGTGAAGGGCATACTCGTTATTCCATTACGGCAGGAGAATACCGTAGTGGAAATGCGCAGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCGGCTGGCTGGACAATATATGGTGGAACGCAACTGGCGGATCGtt                                                                                                                                                                      <  1:204530/250‑1 (MQ=255)                                                          ccGCAGGAAATAGTGTTGACTTGCAGGTAACGATCAAAGAGGCTGACGGCAGCACGCAGATTTTTACCGTACCCAATTCGTCAGTCCCGCTTTTGCAACGTGAAGGGCATACGCACTATTCCATTACGACACGAGGATAACGTCGAGAACATGCGCAGCAGGCAAAACCCCGCATTTTCCAGAGGACATTACACCAACGCCTTCCAGCTGGCTGGCCAATATAtggtggcaagcagatggcgactcgttat                                                                                                                                                                    >  2:53898/1‑229 (MQ=255)                                                           cGCAGGTAATAGTGGTGACTTGCAGGTAACGATCAAAGAGGCTGACGGCAGCACGCAGATTTTTACCGTACCCTATTCGTCAGTCCCGCTTTTGCAACGTGAAGGGCATACTCGTTATTCCATTACGGCAGGAGAATACCGTAGTGGAAATGCGCAGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCGGCTGGCTGGACAATATATGGTGGAACGCAACTGGCGGATCGTTATc                                                                                                                                                                   >  1:88110/1‑251 (MQ=255)                                                                           gacgtgaaGGTAACGAGCAAAGAGGCTGACGGCAGCACGCAGATTGTTAACGTACCCTATTCGTCAGGCCCGCTTGTGCAACGGGAAGGGCATACTAGTTATTCCATTACGGCAGGAGAATACCGTAGTGGAAATGCGCAGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACGTCACGGCCTTCCGGCTGGCTGGACAAGATATGGTGGAACGCAACTGGCGGATCGTTATCGTGCtttgaagctcg                                                                                                                                                    <  2:27645/243‑9 (MQ=255)                                                                                  aGGTAACGATCAAAGAGGCTGACGGCAGCACGCAGATTTTTACCGTACCCTATTCGTCAGTCCCGCTTTTGCAACGTGAAGGGCATACTCGTTATTCCATTACGGCAGGAGAATACCGTAGTGGAAATGCGCAGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCGGCTGGCTGGACAATATATGGTGGAACGCAACTGGCGGATCGTTATCGTGCTTTTAATTTCGGTATCggg                                                                                                                                            <  1:247226/251‑1 (MQ=255)                                                                                         gagcAAAGAGGCTGATGGCAGCGCGCAGATTTTGACCTTACCCTATTCGTCCGTCCCGCTTTTGCAACGTGAAGGGCATACTCGTTATTCCATTACTGCTGTAGAAGACCGTAGTGGAAATGCGCAGCATGAAAATCCCCGCTTTTTACAGAGTACATTTCTCCACGGCCTTCCGGCTGGCTGGACAATATATGGTGGAACGCAACTGGCGGATCGTTATCGTGCTTTTAATTCCGGTATCGGTAAAAACa                                                                                                                                     <  2:327419/248‑1 (MQ=255)                                                                                         gATCAAAGAGGCTGACGGCAGCACGCAGATTTTTACCGTACCCTATTCGTCAGTCCCGCTTTTGCAACGTGAAGGGCATACTCGTTATTCCATTACGGCAGGAGAATACCGTAGTGGAAATGCGCAGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACTCCGCGGCCTTCCGGCTGGCGGGACAATATATGGTGGAACGCAACTGGCGGATCGTTATCGTGCTTTTAATTTCGGTATCGGGAAAAACa                                                                                                                                     <  1:179300/251‑1 (MQ=255)                                                                                                      gACGGCAGCACGCAGATTTTTACCGTCCCCTATTCGTCAGTCCCGCTTTTGCAACGTGAAGGGCATACTCGTTATTCCATTACGGCAGGAGAATACCGTAGTGGAAATGCGCAGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCGGCTGGCTGGACAATATATGGTGGAACGCAACTGGCGGATCGTTATCGTGCTTTTAATTTCGGTATCGGGAAAAACATGGGGGCACTgg                                                                                                                         <  2:198829/250‑1 (MQ=255)                                                                                                                  cAGATTTTTACCGTACCCTATTCGCCAGTCCCGCTTTTGCAACGTGAAGGGCATACTCGTTATTCCATTACGGCAGGAGCATAACGTAATGGAAATGCGCAACAGGAAAAACCCCGCTTTTTCCAGAGGACATTACTCCACGGCCTTCCGGCTGGCTGGAAAATATATGGTGGAAAGCAACTGACGGATCGATATAGTGCTTTTAATTTCAGTATCGGGAAAAACATGGGGGCACTGGGCCCtctgtcttt                                                                                                            >  1:169041/1‑249 (MQ=255)                                                                                                                                                                    gagtACTCGTTATTCCACGACGGCAGGAGAATACCGTAGTGTGAATGCGCAGCATGAAAAACCCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCGGCTGGCTGGACAATATATGGTGGAACGCAACTGGCGGTACGTTATCGATCTTTTAAATTCGGTATTGGGAAAAACATGGGGTCACTGGGCGCTCTGTCTTTGGATATGACGCAGGCTAATTCCACACTTCCCGATGACAGTCAGCATgtcg                                                          <  2:371167/248‑4 (MQ=255)                                                                                                                                                                      atattCGTTATTCCATTACGGCAGGAGAATACCGTAGTGGAAATGCGCAGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCGGCTGGCTGGACAATATATGGTGGAACGCAACTGGCGGATCGTTATCGTGCTTTTAATTTCGGTATCGGGAAAAACATGGGGGCACTGGGCGCTCTGTCTGTGGATATGACGCAGGCTAATTCCACACTTCCCGATGACAGTCAGCATGACGGa                                                        <  1:318803/247‑1 (MQ=255)                                                                                                                                                                            gTTATTCCATTACGTCTGGATAACAACGTAGTGTAAATGTGCAGCAGGAACATCCCCGATGTTTCCAGAGGACATTACTTCTCCGTCTTTCGGCTGGCTGGACAATATATGGTGGCACGTAACTGGCGGAGCGTTATCGTGCTTTTAATTTCGGTATCGGGAAAAACATTGGGTCACTGGGCTCTCTGTCTGTGGATATGACGCAGGCTAATTCCACTCTTCTCGATGACAGTCAGCATGACGGACAATCg                                                  <  2:43369/251‑1 (MQ=255)                                                                                                                                                                            gTTATTCCATTACGGCAGGAGAATACTGTAGTGGAAATGCGCAGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCGGCTGGCTGGACAATATATGGTGGAACGCAACTGGCGGATCGTTATCGTGCTTTTAATTTCGGTATCGGGAAAAACATGGGGGCACTGGGCGCTCTGTCTGTGGATATGATGCATGCTAATTCCACACTTCCCGATGACAGTCAGCATGACGGACAATCg                                                  <  1:20326/251‑1 (MQ=255)                                                                                                                                                                                            aGGAGAATACCGTAGTGGAAATGCGCAGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCGGCTGGCTGGACAATATATGGTGGAACGCAACTGGCGGATCGTTATCGTGCTTTTAATTTCGGTATCGGGAAAAACATGGGGGCACTGGGCGCTCTGTCTGTGGATATGACGCAGGCTAATTCCACACTTCCCGATGACAGTCAGCATGACGGACAATCGGTGCGTTTTCTCtat                                   >  1:202139/1‑250 (MQ=255)                                                                                                                                                                                                      cGTAGTGGAAATGCGCAGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCGGCTGGCTGGACAATATATGGTGGAACGCAACTGGCGGATCGTTATCGTGCTTTTAATTTCGGTATCGGGAAAAACATGGGGGCACTGGGCGCTCTGTCTGTGGATATGACGCAGGCTAATTCCACACTTCCCGATGACAGTCAGCATGACGGACAATCGGTGCGTTTTCTCTATAACAAATCGCt                        >  1:20712/1‑251 (MQ=255)                                                                                                                                                                                                              aaaTGCGCAGCAGGAAAAACCCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCGGCTGGCTGGACAATATATGGTGGAACGCAACTGGCGGATCGTTATCGTGCTTTTAATTTCGGTATCGGGAAAAACATGGGGGCACTGGGCGCTCTGTCTGTGGATATGACGCAGGCTAATTCCACACTTCCCGATGACAGTCAGCATGACGGACAATCGGTGCGTTTTCTCTATAACAAATCGCTCAATGAAt                <  1:24973/251‑1 (MQ=255)                                                                                                                                                                                                                            aaaaacCCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCGGCTGGCTGGACAATATATGGTGGAACGCAACTGGCGGATCGTTATCGTGCTTTTAATTTCGGTATCGGGAAAAACATGGGGGCACTGGGCGCTCTGTCTGTGGATATGACGCAGGCTAATTCCACACTTCCCGATGACAGTCAGCATGACGGACAATCGGTGCGTTTTCTCTATAACAAATCGCTCAATGAATCAGGCACGAATAtt  <  1:221049/251‑1 (MQ=255)                                                                                                                                                                                                                            aaaaacCCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCGGCTGGCTGGACAATATATGGTGGAACGCAACTGGCGGATCGTTATCGTGCTTTTAATTTCGGTATCGGGAAAAACATGGGGGCACTGGGCGCTCTGTCTGTGGATATGACGCAGGCTAATTCCACACTTCCCGAAGACAGTCAGCATGACGGACAATCGGTGCGTTTTCTCTATAACAAATCGCTCAATGAATCAGGAACGAATAtt  >  1:343903/1‑251 (MQ=255)                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                      ATGACATTTATAATAGTACGGTGCCACCGGGGCCTTTTACCATCAACGATATCTATGCCGCAGGTAATAGTGGTGACTTGCAGGTAACGATCAAAGAGGCTGACGGCAGCACGCAGATTTTTACCGTACCCTATTCGTCAGTCCCGCTTTTGCAACGTGAAGGGCATACTCGTTATTCCATTACGGCAGGAGAATACCGTAGTGGAAATGCGCAGCAGGAAAAAACCCGCTTTTTCCAGAGTACATTACTCCACGGCCTTCCGGCTGGCTGGACAATATATGGTGGAACGCAACTGGCGGATCGTTATCGTGCTTTTAATTTCGGTATCGGGAAAAACATGGGGGCACTGGGCGCTCTGTCTGTGGATATGACGCAGGCTAATTCCACACTTCCCGATGACAGTCAGCATGACGGACAATCGGTGCGTTTTCTCTATAACAAATCGCTCAATGAATCAGGCACGAATATT  >  NC_000913/4546048‑4546517

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑