Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	561,696	(G)6→7	coding (2000/2604 nt)	sfmD →	putative fimbrial usher protein SfmD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	561,690	1	.	G	100.0%	85.1 / NA	25	L665R (CTG→CGG)	sfmD	putative fimbrial usher protein SfmD
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base G (12/13);  total (12/13)

CTGGCTGGCAGGTGTAGGTGGGACCTTACTGGAAGGCCACAACCTGAGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCT‑GGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTG  >  NC_000913/561559‑561811                                                                                                                                     |                                                                                                                          ctggctggCAGGTGTAGGTGGGACCTTACTGGAAGGCCACAACCTGAGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCT‑gggggggc                                                                                                                   <  2:238622/140‑3 (MQ=255)      tggcAGGTGTAGGTGGGACCTTACTGGAAGGCCACAACCTGAGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGta                                                                                                               <  2:411439/140‑1 (MQ=255)               tAGGTGGGACCTTACTGGAAGGCCACAACCTGAGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGa                                                                                                      <  2:495321/140‑1 (MQ=255)                 ggTGGGACCTTACTGGAAGGCCACAACCTGAGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGAcc                                                                                                    <  2:108169/140‑1 (MQ=255)                     ggACCTTACTGGAAGGCCACAACCTGAGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGa                                                                                                <  1:395162/140‑1 (MQ=255)                       aCCTTACTGGAAGGCCACAACCTGAGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATc                                                                                              >  1:105235/1‑140 (MQ=255)                       aCCTTACTGGAAGGCCACAACCTGAGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATc                                                                                              >  2:69088/1‑140 (MQ=255)                                  aGGCCACAACCTGAGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGtt                                                                                   >  2:206118/1‑140 (MQ=255)                                     ccACAACCTGAGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAAc                                                                                >  2:240432/1‑140 (MQ=255)                                          aCCTGAGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCa                                                                           >  1:265842/1‑140 (MQ=255)                                                gTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTc                                                                     <  1:83062/140‑1 (MQ=255)                                                                           cGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATgg                                          >  2:401036/1‑140 (MQ=255)                                                                                  tGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACg                                   <  1:206118/140‑1 (MQ=255)                                                                                    ggTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCt                                 <  2:520859/140‑1 (MQ=255)                                                                                    ggTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCt                                 >  1:177367/1‑140 (MQ=255)                                                                                       acacGGGCGGCGCCAGGGCAAACGGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACCGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGag                              >  2:387200/1‑140 (MQ=255)                                                                                        cacGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGagc                             <  1:69088/140‑1 (MQ=255)                                                                                        cacGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGagc                             >  2:422565/1‑140 (MQ=255)                                                                                          cGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGagcca                           >  1:114117/1‑140 (MQ=255)                                                                                          cGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGagcca                           <  2:177367/140‑1 (MQ=255)                                                                                               aGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCtt                      <  2:114117/140‑1 (MQ=255)                                                                                                 cgcCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTa                    <  2:265842/140‑1 (MQ=255)                                                                                                   ccACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAgg                  <  1:401036/140‑1 (MQ=255)                                                                                                      cGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGGTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAggggg               >  2:129513/1‑139 (MQ=255)                                                                                                       ggCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGGATAACCACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTTAGCCAGCCTTTAGGGGAt              >  1:292860/1‑140 (MQ=255)                                                                                                          aaaCTGGCAGGCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATAcc           <  2:11102/140‑1 (MQ=255)                                                                                                                   ggCCGCTTACGGTACGCTGGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTg  >  1:450426/1‑140 (MQ=255)                                                                                                                                     |                                                                                                                          CTGGCTGGCAGGTGTAGGTGGGACCTTACTGGAAGGCCACAACCTGAGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCT‑GGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTG  >  NC_000913/561559‑561811

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑