Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	560,965	C→T	G423G (GGC→GGT)	sfmD →	putative fimbrial usher protein SfmD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	560,965	0	C	T	100.0%	157.8 / NA	49	G423G (GGC→GGT)	sfmD	putative fimbrial usher protein SfmD
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (27/22);  total (27/22)

AATCATCGCCTTTCTTTTTTCAGGGTACGGCACTCGGCGGTTTACCACAGGAATTTACTGCCTACGGCGGGACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGCGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAACACCTTCGGCACCAATTTTCAGTTAATGGGTTACCGCT  >  NC_000913/560829‑561101                                                                                                                                         |                                                                                                                                         aaTCATCGCCTTTCTTTTTTCAGGGTACGGCACTCGGCGGTTTACCACAGGAATTTACTGCCTACGGCGGGACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCa                                                                                                                                       <  2:499496/140‑1 (MQ=255)   tcatcGCCTTTCTTTTTTCAGGGTACGGCACTCGGCGGTTTACCACAGGAATTTACTGCCTACGGCGGGACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAgt                                                                                                                                     <  1:636909/140‑1 (MQ=255)     atcGCCTTTCTTTTTTCAGGGTACGGCACTCGGCGGTTTACCACAGGAATTTACTGCCTACGGCGGGACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAgtgt                                                                                                                                   >  1:204905/1‑140 (MQ=255)        gCCTTTCTTTTTTCAGGGTACGGCACTCGGCGGTTTACCACAGGAATTTACTGCCTACGGCGGGACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGc                                                                                                                                <  1:529195/140‑1 (MQ=255)             tctttTTTCAGGGTACGGCACTCGGCGGTTTACCACAGGAATTTACTGCCTACGGCGGGACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGAt                                                                                                                           >  1:54789/1‑140 (MQ=255)                         gTACGGCACTCGGCGGTTTACCACAGGAATTTACTGCCTACGGCGGGACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATgcg                                                                                                               <  1:1041402/140‑1 (MQ=255)                                  tCGGCGGTTTACCACAGGAATTTACTGCCTACGGCGGGGCGCAATTATCTGCCCATTACACCGCCTTTTTATTAGGGCTCGGGCGCAATCTCGGGAACTGGGGTGCAGGGTTGCTGGATGTAAAGCATGCGCGcagtcag                                                                                                      >  2:435184/1‑140 (MQ=255)                                  tCGGCGGTTTACCACAGGAATTTACTGCCTACGGCGGGACGCAATTATCTGCCAATTACACCGCCTTTTTTTTTGGGCTGGGGCGCAATCTCGGGGAATGGGGTGCAGGGTTGCTGGGTGTAAAGCATGCGCGcagtcag                                                                                                      >  1:122254/1‑140 (MQ=255)                                  tCGGCGGTTTACCACAGGAATTTACTGCCTACGGCGGGACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGcagtcag                                                                                                      >  1:700699/1‑140 (MQ=255)                                   cggcggTTTACCACAGGAATTTACTGCCTACGGCGGGACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGcagtcagt                                                                                                     <  2:155471/140‑1 (MQ=255)                                    ggcggTTTACCACAGGAATTTACTGCCTACGGCGGGAGGGAATTTTCTGCCAATTATATCGGCCTTTTATTAGGGCTGGGGCGCAATTTCGGGAACTGGGGTGGAGTGGTGGTGGGTGTAAGGCATGCGGGCAGTCTGtt                                                                                                    >  2:980004/1‑140 (MQ=255)                                    ggcggTTTACCACAGGAATTTACTGCCTACGGCGGGACGCAATTATCTGCCAATTACACCCCCCTTTTTTTAGGGCTGGGGGGGAATCTTGGGAACTGGGGTGGAGGGTCGCTGGATGTAAATCATGCGCGCAGGCAGtt                                                                                                    >  2:480928/1‑140 (MQ=255)                                      cggTTTACCACAGGAATTTACTGCCTACGGCGGGACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAg                                                                                                  >  2:188250/1‑140 (MQ=255)                                           tACCACAGGAATTTACTGCCTACGGCGGGGCGCAAATATCTTCCCAATACACCCCCCTTTTTTTTTGGGTGGGGGGCAAACTCCGGGACTGGGGGGGAGTGTCGCTGGGTGTAAACCCTGCGCGCAGTCCGTTTACCGAc                                                                                             >  2:781196/1‑140 (MQ=255)                                                caGGAATTTACTGCCTACGGCGGGACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAg                                                                                        >  1:311856/1‑140 (MQ=255)                                                       ttACTGCCTACGGCGGGACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCAt                                                                                 >  1:672028/1‑140 (MQ=255)                                                              cTACGGCGGGACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAggggg                                                                          <  2:204905/140‑1 (MQ=255)                                                               tACGGCGGGACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGa                                                                         <  1:704256/140‑1 (MQ=255)                                                                aCGGCGGGACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGAt                                                                        >  1:183978/1‑140 (MQ=255)                                                                aCGGCGGGACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCACAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGAt                                                                        <  2:759326/140‑1 (MQ=255)                                                                    cggGACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTa                                                                    <  2:54789/140‑1 (MQ=255)                                                                     gggACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTAt                                                                   >  2:148977/1‑140 (MQ=255)                                                                       gACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTc                                                                 >  1:1028615/1‑140 (MQ=255)                                                                          gCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCt                                                              <  1:188250/140‑1 (MQ=255)                                                                              ttATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCct                                                          >  1:898302/1‑140 (MQ=255)                                                                                 tCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTa                                                       >  1:204911/1‑140 (MQ=255)                                                                                   tGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATg                                                     <  2:311856/140‑1 (MQ=255)                                                                                   tGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATg                                                     >  2:86777/1‑140 (MQ=255)                                                                                    gCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGc                                                    >  1:945042/1‑140 (MQ=255)                                                                                     ccAATTACTCCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCg                                                   <  1:993978/140‑1 (MQ=255)                                                                                     ccAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTa                                                                    <  1:954295/123‑1 (MQ=255)                                                                                     ccAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTa                                                                    >  2:954295/1‑123 (MQ=255)                                                                                       aaTTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGaa                                                 <  1:86777/140‑1 (MQ=255)                                                                                        aTTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGaaa                                                <  2:633664/140‑1 (MQ=255)                                                                                        aTTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGaaa                                                >  1:726290/1‑140 (MQ=255)                                                                                               cGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCTTGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGa                                         >  2:950134/1‑140 (MQ=255)                                                                                                 ccTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAac                                       >  2:988356/1‑140 (MQ=255)                                                                                                 ccTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAac                                       <  2:122254/140‑1 (MQ=255)                                                                                                 ccTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAac                                       >  1:605765/1‑140 (MQ=255)                                                                                                  cTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAaca                                      >  1:273616/1‑140 (MQ=255)                                                                                                           aGGGCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAACACCTTCGGCa                             >  2:586993/1‑140 (MQ=255)                                                                                                            gggCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAACACCTTCGGCAc                            >  1:613225/1‑140 (MQ=255)                                                                                                            gggCTGGGGCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAACACCTTCGGCAc                            >  1:402739/1‑140 (MQ=255)                                                                                                                 ggggCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAACACCTTCGGCACCAAtt                       >  2:225691/1‑140 (MQ=255)                                                                                                                  gggCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAACACCTTCGGCACCAAttt                      >  1:722734/1‑140 (MQ=255)                                                                                                                  gggCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAACACCTTCGGCACCAAttt                      <  2:700699/140‑1 (MQ=255)                                                                                                                  gggCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAACACCTTCGGCACCAAttt                      >  2:933017/1‑140 (MQ=255)                                                                                                                   ggCGCAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAACACCTTCGGCACCAAtttt                     <  1:933017/140‑1 (MQ=255)                                                                                                                       cAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAACACCTTCGGCACCAAtttt                     <  1:606036/136‑1 (MQ=255)                                                                                                                       cAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAACACCTTCGGCACCAAtttt                     >  2:606036/1‑136 (MQ=255)                                                                                                                       cAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAACACCTTCGGCACCAATTTTCAGt                 >  1:2678/1‑140 (MQ=255)                                                                                                                       cAATCTCGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAACACCTTCGGCACCAATTTTCAGt                 >  1:216178/1‑140 (MQ=255)                                                                                                                           ctcGGGAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAACACCTTCGGCACCAATTTTCAGTTAAt             <  2:898302/140‑1 (MQ=255)                                                                                                                              gggAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAACACCTTCGGCACCAATTTTCAGTTAATggg          <  2:183978/140‑1 (MQ=255)                                                                                                                               ggAACTGGGGTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAACACCTTCGGCACCAATTTTCAGTTAATGGGt         <  1:148977/140‑1 (MQ=255)                                                                                                                                      gggTGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAACACCTTCGGCACCAATTTTCAGTTAATGGGTTACCGCt  >  2:811337/1‑140 (MQ=255)                                                                                                                                         |                                                                                                                                         AATCATCGCCTTTCTTTTTTCAGGGTACGGCACTCGGCGGTTTACCACAGGAATTTACTGCCTACGGCGGGACGCAATTATCTGCCAATTACACCGCCTTTTTATTAGGGCTGGGGCGCAATCTCGGGAACTGGGGCGCAGTGTCGCTGGATGTAACGCATGCGCGCAGTCAGTTAGCCGACGCCAGTCGTCATGAGGGGGATTCTATTCGCTTCCTCTATGCGAAATCGATGAACACCTTCGGCACCAATTTTCAGTTAATGGGTTACCGCT  >  NC_000913/560829‑561101

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: ‑