Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,184,461	T→C	F157F (TTT→TTC)	yqiI →	fimbrial protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,184,461	0	T	C	84.4%	70.3 / ‑0.0	32	F157F (TTT→TTC)	yqiI	fimbrial protein
Reads supporting (aligned to +/- strand):  ref base T (5/0);  new base C (10/17);  total (15/17)
Fisher's exact test for biased strand distribution p-value = 1.49e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

GATTATGATTCTACATCTCCACTACCTATTGCAGCACCTGTATGTATTGATATAAAGGGAGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTTCCAGTACGAGTGCAGCTATATATTAAGCTAGCTAAAAATGCCAATAAAGTAAATAAAAAACTTGTATTACCTGACGAATATATAGCACTTGAATTTAAAGGTATGAGCGGAGCAGG  >  NZ_CP009273/3184324‑3184577                                                                                                                                          |                                                                                                                     gATTATGATTCTACATCTCCACTACCTATTGCAGCACCTGTATGTATTGATATAAAGGGAGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTTGAACGCGATTATCAGTAACTTTTc                                                                                                                     >  1:138171/1‑139 (MQ=255)        tttCTACATCTCCACTACCTATTGCAGCACCTGTATGTATTGATATAAAGGGAGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTCCCAGTAc                                                                                                               <  2:248689/137‑1 (MQ=255)           cTACATCTCCACTACCTATTGCAGCACCTGTATGTATTGATATAAAGGGAGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTCCCAGTACGAg                                                                                                            <  1:183553/138‑1 (MQ=255)            tACATCTCCACTACCTATTGCAGCACCTGTATGTATTGATATAAAGGGAGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAAACGCAATTATTAGTAACTTTTCCCGTACGAGTg                                                                                                          >  2:251287/1‑139 (MQ=255)                 ctcCACTACCTATTGCAGCACCTGTATGTATTGATATAAAGGGAGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCCATTATCAGTAAATTTCCCCGTACGGGGGCAGCt                                                                                                     >  2:488628/1‑139 (MQ=255)                             ttGCAGCACCTGTATGTATTGATATAAAGGGAGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTTCTGGAACGCAATTATTAGAAAACTTTCCCATACGAGGGGAGCTATATATTAaact                                                                                         >  2:5767/1‑139 (MQ=255)                             ttGCAGCACCTGTATGTATTGATATAAAGGGAGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTCCCAGTACGAGTGCAGCTATATATTAag                                                                                           <  1:77638/137‑1 (MQ=255)                              tGCAGCACCTGTATGTATTGATATAAAGGGAGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTCCCCGTACGAGTg                                                                                                          >  1:168156/1‑121 (MQ=255)                              tGCAGCACCTGTATGTATTGATATAAAGGGAGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTCCCAGTACGAGTg                                                                                                          <  2:168156/121‑1 (MQ=255)                              tGCAGCACCTGTATGTATTGATATAAAGGGAGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGGCCTGAACCGCAATTATCAATAACTTTCCCCGTACGAGTGCAGCTATATAtttaact                                                                                         >  2:521835/1‑133 (MQ=255)                                   caCCTGTATGTATTGATATAAAGGGAGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTccc                                                                                                                    <  2:440960/106‑1 (MQ=255)                                   caCCTGTATGTATTGATATAAAGGGAGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTTcc                                                                                                                    >  1:440960/1‑106 (MQ=255)                                   caCCTGTATGTATTGATATAAAGGGAGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTCCCCGTACGAGGGCAGCTATATATTTAgctagcta                                                                                    >  2:511138/1‑138 (MQ=255)                                   caCCTGTATGTATTGATATAAAGGGAGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAAACGCAATTATCAATAACTTTTCCCGGACGAGTGCAGGTATATATTAAactagcta                                                                                    >  2:77638/1‑138 (MQ=255)                                                   tataAAGGGAGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTTAACCCCACTTATTACTTACCTTCTCCTTACTAGTTGAACTTTATATTAATCTATCTAAAAATTCCAACaaact                                                                    >  1:231917/1‑136 (MQ=255)                                                            aGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTCCCCGTACGAGTGCAGCTATATATTAAGCTAGCTAAAAATGCCAATAAAGTAAATaaaaaa                                                          >  1:488795/1‑139 (MQ=255)                                                            aGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTCCCAGTACGAGTGCAGCTATATATTAAGCTAGCTAAAAATGCCAATAAAGTAAATaaaaaa                                                          <  2:355666/139‑1 (MQ=255)                                                            aGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTCCCAGTACGAGTGCAGCTATATATTAAGCTAGCTAAAAATGCCAATAAAGTAAATaaaaaa                                                          <  2:355658/139‑1 (MQ=255)                                                            aGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTCCCAGTACGAGTGCAGCTATATATTAAGCTAGCTAAAAATGCCAATAAAGTAAATaaaaaa                                                          <  1:488628/139‑1 (MQ=255)                                                             gCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTCCCAGTACGAGTGCAGCTATATATTAAGCTAGCTAAAAATGCCAATAAAGTAAATAAAAAAc                                                         <  2:488795/139‑1 (MQ=255)                                                             gCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAAACCCAATTTTCAGTAACTTTCCCCGTACGTGGGCAGCTATATATTAAGATAACTAAAAAAACCaataaaaaaaataaaaaaa                                                         >  2:449724/1‑138 (MQ=255)                                                                        cGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTCCCAGTACGAGTGCAGCTATATATTAAGCTAGCTAAAAATGCCAATAAAGTAAATAAAAAACTTGTATTAc                                                <  2:572301/137‑1 (MQ=255)                                                                         gggAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTCCCAGTACGAGTGCAGCTATATATTAAGCTAGCTAAAAATGCCAATAAAGTAAATAAAAAACTTGTATTACCt                                              <  1:251287/138‑1 (MQ=255)                                                                          ggAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTCCCAGTACGAGTGCAGCTATATATTAAGCTAGCTAAAAATGCCAATAAAGTAAATAAAAAACTTGTATTACCTGa                                            <  1:511138/139‑1 (MQ=255)                                                                             aTGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTCCCAGTACGAGTGCAGCTATATATTAAGCTAGTTAAAAATGCCAATAAAGTAAATAAAAAACTTGTATTACCTGACGa                                         <  2:198472/139‑1 (MQ=255)                                                                                gCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGGACCCCCCTTATATGTAACTTTCCCAGTACACGTGCAGCTATATATTAAGCTTACTAAAAATGCCCATAAAATAAATATAAAACCTTTATTTCCTTACGtata                                      >  1:220449/1‑139 (MQ=255)                                                                                                    tGTAGTGGCGGTCCTGAACCCCAATTATCAGTAACTTTCCCCGGACGAGGGGAACCATATATTAAGCTAGCTAAAAAAGCCAATAAAATAAATAAAAAAATTGTATTAACTGACGAAAATATAGCACTTTAAtttta                    >  2:557083/1‑135 (MQ=255)                                                                                                      tAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTCCCAGTACGAGTGCAGCTATATATTAAGCTAGCTAAAAATGCCAATAAAGTAAATAAAAAACTTGTATTACCTGACGAATATATAGCACTTGAATTTaaa                   <  1:455207/136‑1 (MQ=255)                                                                                                      tAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTCCCAGTACGAGTGCAGCTATATATTAAGCTAGCTAAAAATGCCAATAAAGTAAATAAAAAACTTGTATTACCTGACGAATATATAGCACTTGAATTTaaa                   <  1:188743/136‑1 (MQ=255)                                                                                                      tAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTCCCAGTACGAGTGCAGCTATATATTAAGCTAGCTAAAAATGCCAATAAAGTAAATAAAAAACTTGTATTACCTGACGAATATATAGCACTTGAATTTAAAGGt                <  1:557083/139‑1 (MQ=255)                                                                                                          ggCGGTCCTGAAACGCAATTTTCAGTAAATTTCCCCGGAAGAGTGGAGCCATATATTAAGCTAGCTAAAAAATCCAATAAAATAAATAAAAAAATTGTATTACCTGACGAATATATAGCACTTGAATTTaaaaagat              >  2:425767/1‑132 (MQ=255)                                                                                                            cGGTCCTGAACCGCAATTATCAGTAACTTTCCCAGTACGAGTGCAGCTATATATTAAGCTAGCTAAAAATGCCAATAAAGTAAATAAAAAACTTGTATTACCTGACGAATATATAGCACTTGAATTTAAAGGTATGAGc          <  1:425767/139‑1 (MQ=255)                                                                                                                    aaCCGCAATTATCAGTAACTTTCCCAGTACGAGTGCAGCTATATATTAAGCTAGCTAAAAATGCCAATAAAGTAAATAAAAAACTTGTATTACCTGACGAATATATAGCACTTGAATTTAAAGGTATGAGCGGAGCAgg  <  1:521835/139‑1 (MQ=255)                                                                                                                                          |                                                                                                                     GATTATGATTCTACATCTCCACTACCTATTGCAGCACCTGTATGTATTGATATAAAGGGAGCCGGAACCTTCGGGAATGGCTACAAAAAGCCCGCAGTCTGTAGTGGCGGTCCTGAACCGCAATTATCAGTAACTTTTCCAGTACGAGTGCAGCTATATATTAAGCTAGCTAAAAATGCCAATAAAGTAAATAAAAAACTTGTATTACCTGACGAATATATAGCACTTGAATTTAAAGGTATGAGCGGAGCAGG  >  NZ_CP009273/3184324‑3184577

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑