Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_007779	4,547,544	T→C	100%	intergenic (+231/‑251)	fimE → / → fimA	type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007779	4,547,544	0	T	C	100.0%	79.0 / NA	25	intergenic (+231/‑251)	fimE/fimA	type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (14/11);  total (14/11)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAG  >  NC_007779/4547329‑4547768                                                                                                                                                                                                                        |                                                                                                                                                                                                                                 ataaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCa                                                                                                                                                                                                           <  1:789755/239‑1 (MQ=255)                cAAATAAAGACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATCTTAAAAAACGACAAAAAGCATCTAACTGTTGGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACTTTTCTGTGGCTCGACGCATCTTCCTCACTCGTCTCTCCAAAAACCACCTCATGCAATATAAACATc                                                                                                                                                                                            <  2:802869/239‑1 (MQ=255)                               cAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGAt                                                                                                                                                                               <  2:1196/237‑1 (MQ=255)                                  ttGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACaa                                                                                                                                                                          >  2:709049/1‑239 (MQ=255)                                      ggCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAg                                                                                                                                                                       <  1:1058940/238‑1 (MQ=255)                                       gCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACCATAGaa                                                                                                                                                                     >  1:652157/1‑239 (MQ=255)                                                 ccATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGcc                                                                                                                                                            <  1:698766/238‑1 (MQ=255)                                                  cATATCATAAATAAGTTACGTATTTTTTCTCAAACATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCcaa                                                                                                                                                          <  2:1439734/239‑1 (MQ=255)                                                                                             atTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATg                                                                                                                                                                                                         <  1:408926/149‑1 (MQ=255)                                                                                              ttAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGttt                                                                                                                                      >  2:411214/1‑215 (MQ=255)                                                                                              ttAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGttt                                                                                                                                      <  1:411214/215‑1 (MQ=255)                                                                                              ttAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGCAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAg                                                                                                              >  1:287860/1‑239 (MQ=255)                                                                                                       gACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGCAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGAACCATCTTCCTCACTCTTCCCTCCAAAAACCACCCCATTCAATACAAAc                                                                                                                                                                                               >  2:408926/1‑149 (MQ=255)                                                                                                                                            tCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAg                                                                >  1:90644/1‑239 (MQ=255)                                                                                                                                                ttGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGtt                                                            >  2:1322471/1‑239 (MQ=255)                                                                                                                                                     aattaattTCCCATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCGCCTCATGCAATATAAACATCTataaata                                                                                                                                                                                    <  2:132098/114‑1 (MQ=255)                                                                                                                                                     aattaattTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTataaata                                                                                                                                                                                    >  1:132098/1‑114 (MQ=255)                                                                                                                                                             tCACGTCACCTCCGCTATATGTAAATCTAACGTTTCGGTGGCTCGACACATCTACCTCACTCGTCTCACCAAAAACCACCTCATTCAATATAAACATGTATAAATAAATAGAACAATGGAATAATAAGGCAACAAGTAAACTGAAAAAGTTTGTCCGCGATGCTTTCAGCTATGAGTCAAAATGGCGCCAAAAGTTTCATCTTGTGCGGGAAAACTCTGCAGTGTTGGCAGTCAAACTc                                               <  2:652157/239‑1 (MQ=255)                                                                                                                                                                                tGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAgtgt                             >  1:176797/1‑238 (MQ=255)                                                                                                                                                                                tGTAAAGCTAACGTTTCTGTGGCTCGACGCATCCTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGGCAAACTCGTTTACAAAACAAAGGGTa                            >  2:72013/1‑239 (MQ=255)                                                                                                                                                                                          aCGTTTCTGTGGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACt                  >  2:27526/1‑239 (MQ=255)                                                                                                                                                                                                 tgtgGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGaaaa                                                                        >  2:131647/1‑178 (MQ=255)                                                                                                                                                                                                 tgtgGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGaaaa                                                                        <  1:131647/178‑1 (MQ=255)                                                                                                                                                                                                 tgtgGCTCGACGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATg           >  1:720724/1‑239 (MQ=255)                                                                                                                                                                                                          aCGCATCTTCCTCACTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAg  >  1:1105257/1‑239 (MQ=255)                                                                                                                                                                                                                        |                                                                                                                                                                                                                                 ATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAG  >  NC_007779/4547329‑4547768

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑