Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 562,090 A→G S798S (TCA→TCG)  sfmD → putative fimbrial usher protein SfmD

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913562,0900AG76.5% 88.1 / 26.2 51S798S (TCA→TCG) sfmDputative fimbrial usher protein SfmD
Reads supporting (aligned to +/- strand):  ref base A (6/6);  new base G (15/24);  total (21/30)
Fisher's exact test for biased strand distribution p-value = 5.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.53e-01

CATCGATGTTGAAAAAAATATTAGCAGCGTTGTGCCGACGCAAGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCACTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTCAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCAC  >  NC_000913/561955‑562225
                                                                                                                                       |                                                                                                                                       
cATCGATGTTGAAAAAAATATTAGCAGCGTTGTGCCGACGCAAGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCGTTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTgg                                                                                                                                     <  1:403356/140‑1 (MQ=255)
cATCGATGTTGAAAAAAATATTAGCAGCGTTGTGCCGACGCAAGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTgg                                                                                                                                     >  2:300049/1‑140 (MQ=255)
         tGAAAAAAATATTAGCAGCGTTGTGCCGACGCAAGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGaaa                                                                                                                            >  2:374278/1‑140 (MQ=255)
          gAAAAAAATATTAGCAGCGTTGTGCCGACGCAAGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGaaaa                                                                                                                           <  2:90542/140‑1 (MQ=255)
          gAAAAAAATATTAGCAGCGTTGTGCCGACGCAAGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGaaaa                                                                                                                           >  1:361180/1‑140 (MQ=255)
                     tAGCAGCGTTGTGCCGACGCAAGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGaa                                                                                                                >  2:692857/1‑140 (MQ=255)
                     tAGCAGCGTTGTGCCGACGCAAGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGaa                                                                                                                >  2:485142/1‑140 (MQ=255)
                      agcagcGTTGTGCCGACGCAAGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAAt                                                                                                               <  2:704077/140‑1 (MQ=255)
                      agcagcGTTGTGCCGACGCAAGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCACTGGTACGGGAAAACAGTACCGGAAt                                                                                                               <  2:154246/140‑1 (MQ=255)
                           cGTTGTGCCGACGCAAGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGTGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAAcc                                                                                                           <  1:572986/139‑1 (MQ=255)
                           cGTTGTGCCGACGCAAGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGTGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAAcc                                                                                                           >  2:572986/1‑139 (MQ=255)
                           cGTTGTGCCGACGCAAGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCACTGGTACGGGAAAAc                                                                                                                          <  1:582427/124‑1 (MQ=255)
                           cGTTGTGCCGACGCAAGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCACTGGTACGGGAAAAc                                                                                                                          >  2:582427/1‑124 (MQ=255)
                                tgCCGACGCAAGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTAtg                                                                                                     >  2:495577/1‑140 (MQ=255)
                                      cGCAAGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATggtgggt                                                                                               >  2:768089/1‑140 (MQ=255)
                                          aGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGtgatg                                                                                           >  2:225604/1‑140 (MQ=255)
                                          aGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGtgatg                                                                                           >  1:342065/1‑140 (MQ=255)
                                          aGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCACTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGtgatg                                                                                           >  1:435508/1‑140 (MQ=255)
                                           ggCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGtgatga                                                                                          <  2:575188/140‑1 (MQ=255)
                                                gTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGc                                                                                     <  2:75869/140‑1 (MQ=255)
                                                gTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGc                                                                                     <  1:659657/140‑1 (MQ=255)
                                                gTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCACTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGc                                                                                     >  2:591889/1‑140 (MQ=255)
                                                   ggTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAg                                                                                  <  1:485142/140‑1 (MQ=255)
                                                    gTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGt                                                                                 <  1:785812/140‑1 (MQ=255)
                                                    gTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACAAGTATGGTGGGTGATGACGGGCAAGt                                                                                 <  1:557442/140‑1 (MQ=255)
                                                     ttCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGtt                                                                                <  2:42360/140‑1 (MQ=255)
                                                          gCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGtttattt                                                                           <  2:342065/140‑1 (MQ=255)
                                                             aaTTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAg                                                                        <  2:527327/140‑1 (MQ=255)
                                                             aaTTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAg                                                                        <  2:136711/140‑1 (MQ=255)
                                                                 ttGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAgtggt                                                                    <  1:623182/140‑1 (MQ=255)
                                                                    aTACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCACTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTgcg                                                                 <  2:187663/140‑1 (MQ=255)
                                                                       cccGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCACTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCa                                                              <  1:591889/140‑1 (MQ=255)
                                                                          gCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTg                                                           >  2:797005/1‑140 (MQ=255)
                                                                                  gTGCGGGCGCTCATTACCGTTACTCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGTAAGACAGTACCGGAATAACCAGGATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGGCATTGTCTGGTGa                                                   >  2:549553/1‑140 (MQ=255)
                                                                                    gCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGTGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAAt                                                 >  2:149264/1‑140 (MQ=255)
                                                                                       ggCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCACTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTAc                                              <  2:435508/140‑1 (MQ=255)
                                                                                          gcTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTgg                                           >  2:761467/1‑140 (MQ=255)
                                                                                          gcTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCACTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTgg                                           >  2:627802/1‑140 (MQ=255)
                                                                                             cATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTc                                        <  1:311746/140‑1 (MQ=255)
                                                                                             cATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTc                                        <  1:300049/140‑1 (MQ=255)
                                                                                                            gggCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTCAGTGGGGAGACGgcg                         >  2:341778/1‑140 (MQ=255)
                                                                                                            gggCGGAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTCAGTGGGGAGACGgcg                         >  2:79750/1‑140 (MQ=255)
                                                                                                            gggCGGAAAACCGGTGCCGTTTGGATCACTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTgg                                           <  1:642494/122‑1 (MQ=255)
                                                                                                            gggCGGAAAACCGGTGCCGTTTGGATCACTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTgg                                           >  2:642494/1‑122 (MQ=255)
                                                                                                             ggCGGAAAACCGGTGCCGTTTGGATCACTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTCAGTGGGGAGACGgcgc                        >  1:259920/1‑140 (MQ=255)
                                                                                                                 gAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTCAGTGGGGAGACGGCGCGAAc                    <  2:361180/140‑1 (MQ=255)
                                                                                                                 gAAAACCGGTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTCAGTGGGGAGACAGCGCGAAc                    <  1:768089/140‑1 (MQ=255)
                                                                                                                        ggTGCCGTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTCAGTGGGGAGACGGCGCGAACTCACGCt             <  2:762222/140‑1 (MQ=255)
                                                                                                                              gTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTCAGTGGGGAGACGGCGCGAACTCACGCTGCATTg       <  1:341778/140‑1 (MQ=255)
                                                                                                                              gTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTCAGTGGGGAGACGGCGCGAACTCACGCTGCATTg       <  1:374278/140‑1 (MQ=255)
                                                                                                                              gTTTGGATCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTCAGTGGGGAGACGGCGCGAACTCACGCTGCATTg       <  1:253121/140‑1 (MQ=255)
                                                                                                                                    aTCGCTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTCAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCAc  <  1:104570/139‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                       
CATCGATGTTGAAAAAAATATTAGCAGCGTTGTGCCGACGCAAGGCGCGTTGGTTCGTGCCAATTTTGATACCCGCATAGGCGTGCGGGCGCTCATTACCGTTACCCAGGGCGGAAAACCGGTGCCGTTTGGATCACTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTCAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCAC  >  NC_000913/561955‑562225

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑