Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,414,715 T→C 15.2% L165S (TTG→TCG)  yitU_2 → 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase YitU

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,414,7150TC15.2% 96.0 / 10.6 39L165S (TTG→TCG) yitU_25‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase YitU
Reads supporting (aligned to +/- strand):  ref base T (11/22);  new base C (3/3);  total (14/25)
Fisher's exact test for biased strand distribution p-value = 6.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTAGATCCACATAAGCTGGCCAGTTGTATTGATGTTGCAAATATCGACACACCAATCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAAATATACTGCATTACAATATATATTTGATGCAGATGTTAAATATATAGCATTTGGTAATGACCACAATGATATTGT  >  USA300TCH1516_ALE/1414582‑1414850
                                                                                                                                     |                                                                                                                                       
ttAGATCCACATAAGCTGGCCAGTTGTATTGATGTTGCAAATATCGACACACCAATCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATg                                                                                                                                  <  2:55955/141‑1 (MQ=255)
      ccACATAAGCTGGCCAGTTGTATTGATGTTGCAAATATCGACACACCAATCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCAc                                                                                                                            <  1:139213/141‑1 (MQ=255)
        acaTAAGCTGGCCAGTTGTATTGATGTTGCAAATATCGACACACCAATCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCa                                                                                                                          <  1:21879/141‑1 (MQ=255)
                 ggCCAGTTGTATTGATGTTGCAAATATCGACACACCAATCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGa                                                                                                                 >  1:287014/1‑141 (MQ=255)
                   ccAGTTGTATTGATGTTGCAAATATCGACACACCAATCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGt                                                                                                               <  2:335772/141‑1 (MQ=255)
                   ccAGTTGTATTGATGTTGCAAATATCGACACACCAATCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGt                                                                                                               <  2:340714/141‑1 (MQ=255)
                   ccAGTTGTATTGATGTTGCAAATATCGACACACCAATCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGt                                                                                                               <  2:376447/141‑1 (MQ=255)
                   ccAGTTGTATTGATGTTGCAAATATCGACACACCAATCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGt                                                                                                               <  2:51201/141‑1 (MQ=255)
                    cAGTTGTATTGATGTTGCAAATATCGACACACCAATCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGta                                                                                                              <  2:460134/141‑1 (MQ=255)
                    cAGTTGTATTGATGTTGCAAATATCGACACACCAATCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGta                                                                                                              <  1:342171/141‑1 (MQ=255)
                             tGATGTTGCAAATATCGACACACCAATCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGa                                                                                                     <  1:110576/141‑1 (MQ=255)
                             tGATGTTGCAAATATCGACACACCAATCAAGATTATGTTATTAAATATAGACCCTGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCAGCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGa                                                                                                     <  2:366240/141‑1 (MQ=255)
                                     cAAATATCGACACACCAATCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAg                                                                                             >  1:150056/1‑141 (MQ=255)
                                       aaTATCGACACACCAATCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATCGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAgcg                                                                                           >  1:308339/1‑141 (MQ=255)
                                       aaTATCGACACACCAATCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATCGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAgcg                                                                                           >  1:334982/1‑141 (MQ=255)
                                       aaTATCGACACACCAATCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATCGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAgcg                                                                                           >  1:263753/1‑141 (MQ=255)
                                                   ccAATCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAAc                                                                               <  2:45616/141‑1 (MQ=255)
                                                     aaTCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATGCCATCAAGAATTGGAAATGATGCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACaa                                                                             <  2:424132/141‑1 (MQ=255)
                                                     aaTCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACaa                                                                             <  2:405268/141‑1 (MQ=255)
                                                       tCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAAat                                                                           >  1:413535/1‑141 (MQ=255)
                                                                      taAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAAATATACTGCATTACAat                                                            >  1:272496/1‑141 (MQ=255)
                                                                         atatAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAAGTTTTAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGGAAAATATTAACAAATATACTGCATTACAatata                                                         <  1:240907/141‑1 (MQ=255)
                                                                                   ggCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAAATATACTGCATTACAATATATATTTGATGc                                               <  1:76403/141‑1 (MQ=255)
                                                                                   ggCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAAATATACTGCATTACAATATATATTTGATGc                                               <  1:126550/141‑1 (MQ=255)
                                                                                    gCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAAATATACTGCATTACAATATATATTTGATGCa                                              <  2:70900/141‑1 (MQ=255)
                                                                                    gCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAAATATACTGCATTACAATATATATTTGATGCa                                              <  2:2808/141‑1 (MQ=255)
                                                                                    gCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAAATATACTGCATTACAATATATATTTGATGCa                                              <  1:395181/141‑1 (MQ=255)
                                                                                    gCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCACAAAATATTAACAAATATACTGCATTACAATATATATTTGATGCa                                              <  2:152426/141‑1 (MQ=255)
                                                                                    gCACAAATTACAACTATATTAGACGAGCTAGATAAATACCAACAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAAATATACTGCATTACAATATATATTTGATGCa                                              <  1:289211/141‑1 (MQ=255)
                                                                                      acaAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAAATATACTGCATTACAATATATATTTGATGCAGa                                            >  2:190636/1‑141 (MQ=255)
                                                                                                                     aaaTACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAAATATACTGCATTACAATATATATTTGATGCAGATGTTAAATATATAGCATTTGGTAATGACcac             >  2:211386/1‑141 (MQ=255)
                                                                                                                     aaaTACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAAATATACTGCATTACAATATATATTTGATGCAGATGTTAAATATATAGCATTTGGTAATGACcac             >  2:367882/1‑141 (MQ=255)
                                                                                                                         aCCATCAAGAATCGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAGATATAATGCATTACAATATATATTTGATGCAGATGTTAAATATATAGCATTTGGTAATGACCACAATg         <  2:334982/141‑1 (MQ=255)
                                                                                                                         aCCATCAAGAATCGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAAATATACTGCATTACAATATATATTTGATGCAGATGTTAAATATATAGCATTTGGTAATGACCACAATg         <  2:308339/141‑1 (MQ=255)
                                                                                                                         aCCATCAAGAATCGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAAATATACTGCATTACAATATATATTTGATGCAGATGTTAAATATATAGCATTTGGTAATGACCACAATg         <  2:263753/141‑1 (MQ=255)
                                                                                                                           cATCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAAATATACTGCATTACAATATATATTTGATGCAGATGTTAAATATATAGCATTTGGTAATGACCACAATGat       >  2:204730/1‑141 (MQ=255)
                                                                                                                               gaGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAAATATACTGCATTACAATATATATTTGATGCAGATGTTAAATATATAGCATTTGGTAATGACCACAATGATATTg   >  1:436721/2‑141 (MQ=255)
                                                                                                                               aaGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAAAAGCGCAAAATATAAACAAATATACTGCATTACAATATATATTTGATGCAGATGTTAAATATATAGCATTTGGTAATGACCACAATGATATTg   >  1:159641/1‑141 (MQ=255)
                                                                                                                                aGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAAATATACTGCATTACAATATATATTTGATGCAGATGTTAAATATATAGCATTTGGTAATGACCACAATGATATTGt  >  1:20151/1‑141 (MQ=255)
                                                                                                                                     |                                                                                                                                       
TTAGATCCACATAAGCTGGCCAGTTGTATTGATGTTGCAAATATCGACACACCAATCAAGATTATTTTATTAAATATAGACCCGGCACAAATTACAACTATATTAGACGAGCTAGATAAATACCATCAAGAATTGGAAATGATTCACCATTCAAATGAGTATAACATTGATATAACAGCGCAAAATATTAACAAATATACTGCATTACAATATATATTTGATGCAGATGTTAAATATATAGCATTTGGTAATGACCACAATGATATTGT  >  USA300TCH1516_ALE/1414582‑1414850

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑