Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 973,213 C→A 100% E175* (GAG→TAG)  yitU_1 ← 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_ALE973,2130CA100.0% 161.8 / ‑6.5 52E175* (GAG→TAG) yitU_15‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase YitU
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base A (30/20);  total (32/20)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCTTCATCACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGATTACCCA  >  USA300TCH1516_ALE/973077‑973350
                                                                                                                                        |                                                                                                                                         
tCTTCATCACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACGTGGTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGGCAGGGAATCGGGCGCGCAGCCGTCGATGCTGaaga                                                                                                                                       >  1:182569/1‑139 (MQ=255)
  ttCATCACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATg                                                                                                                                     <  2:478838/141‑1 (MQ=255)
   tcatcaCCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGa                                                                                                                                    >  1:247320/1‑141 (MQ=255)
   tcatcaCCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGa                                                                                                                                    >  2:103308/1‑141 (MQ=255)
   tcatcaCCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGa                                                                                                                                    >  1:616632/1‑141 (MQ=255)
    catcaCCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATCACAGTGTATGTTGCGCCCCAGCGTCGATGCTAAATATGAt                                                                                                                                   >  1:596293/1‑141 (MQ=255)
         ccGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCa                                                                                                                              >  1:92615/1‑141 (MQ=255)
         ccGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCACCGTCGATGCTAAATATGATCGGCa                                                                                                                              <  1:28574/141‑1 (MQ=255)
             aTGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATaaa                                                                                                                          >  1:359775/1‑141 (MQ=255)
                   taataTTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCCCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAg                                                                                                                    >  1:189169/1‑141 (MQ=255)
                         tattTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCa                                                                                                              <  1:577957/141‑1 (MQ=255)
                               ggTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATAtttt                                                                                                        <  2:473288/141‑1 (MQ=255)
                                    atatTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGAtt                                                                                                   >  1:474314/1‑141 (MQ=255)
                                    atatTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTGACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAGATGAGTAAGCATATTTTTGAtt                                                                                                   >  2:249125/1‑141 (MQ=255)
                                       tttAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCa                                                                                                <  2:130448/141‑1 (MQ=255)
                                       tttAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCa                                                                                                <  1:773995/141‑1 (MQ=255)
                                       attAAAAATTGTTTAACTTGCTTAAAGCCTCTTGCTTTATTAATACCAAGCTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATAAAAAAAAAAAAAAAATGAGTAAGCATATTTTTGATTTCa                                                                                                <  2:55410/140‑1 (MQ=255)
                                        ttAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAAAGCCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAg                                                                                               >  2:319758/1‑141 (MQ=255)
                                           aaaaTTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTa                                                                                            <  1:578714/141‑1 (MQ=255)
                                            aaaTTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTAt                                                                                           >  1:346185/1‑141 (MQ=255)
                                            aaaTTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTAt                                                                                           >  2:232271/1‑141 (MQ=255)
                                                     aaCTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTttc                                                                                  <  1:219309/141‑1 (MQ=255)
                                                     aaCCTGCTCAATGCCTCTTGCTTTATTAAAACCAAGCTATACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTttc                                                                                  <  1:35956/141‑1 (MQ=255)
                                                         tGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAACTGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCg                                                                              >  2:279003/1‑141 (MQ=255)
                                                          gCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCgg                                                                             >  2:437999/1‑141 (MQ=255)
                                                               aTGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCa                                                                        <  1:738584/141‑1 (MQ=255)
                                                                tGCCTCTTGCTTTATGAATTCCAGGTTTTACAATTTGAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAGATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCaa                                                                       <  2:607554/141‑1 (MQ=255)
                                                                    tctTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTaa                                                                   <  1:584951/141‑1 (MQ=255)
                                                                       tGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATAAAAATGAGTAAGCCTATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTACAAt                                                                >  2:211683/1‑141 (MQ=255)
                                                                        gCTTTATTAATACCAAGTTTTACAATTTCAATGAAAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCACTTAAAAtt                                                               >  2:708941/1‑141 (MQ=255)
                                                                                    ccAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGATAGGGGAt                                                   >  2:156302/1‑141 (MQ=255)
                                                                                        gTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCtt                                               <  2:475862/141‑1 (MQ=255)
                                                                                          tttACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTc                                             >  2:92490/1‑141 (MQ=255)
                                                                                          tttACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGAAGGGGATTCTTTc                                             >  1:289823/1‑141 (MQ=255)
                                                                                          tttACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTAATTTCTTCGGCTTCAATTAACATTGAGGTAGGGGATTCTTTc                                             >  2:210128/1‑141 (MQ=255)
                                                                                             aCAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTCTTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAg                                          >  1:364736/1‑141 (MQ=255)
                                                                                              cAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGt                                         >  2:563663/1‑141 (MQ=255)
                                                                                                  ttCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGAc                                     >  1:355228/1‑141 (MQ=255)
                                                                                                    cAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGGTTCTTTCAAGTGGACaa                                   >  2:264653/1‑141 (MQ=255)
                                                                                                    cAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACaa                                   >  1:380542/1‑141 (MQ=255)
                                                                                                       tgtcAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTa                                <  2:189169/138‑1 (MQ=255)
                                                                                                                aTGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATCAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAACATTGAGGTAGGGGATTCTTTCAAGAGGACAAGTAAATTACCAg                       >  2:383452/1‑141 (MQ=255)
                                                                                                                aTGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATAAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAATAAATTACCAg                       >  2:383809/1‑141 (MQ=255)
                                                                                                                    tGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTg                   >  2:172548/1‑141 (MQ=255)
                                                                                                                    tGCCCCACAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTg                   <  1:38985/141‑1 (MQ=255)
                                                                                                                      cgcCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGaa                 >  2:505796/1‑141 (MQ=255)
                                                                                                                        ccccAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAAtt               >  2:371647/1‑141 (MQ=255)
                                                                                                                              cGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATAGTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGa         <  1:319758/141‑1 (MQ=255)
                                                                                                                               gTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTATCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGAt        >  1:434494/1‑141 (MQ=255)
                                                                                                                                    tGCTAAATATTATCGGGATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGATTAccc   <  2:266257/141‑1 (MQ=255)
                                                                                                                                     gCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGATTACCCa  <  1:172592/141‑1 (MQ=255)
                                                                                                                                     gCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTGGATTTCAGTTATTTGACTTTCTTCGGCTTCAATTAGAATTGAGGTAGGTGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTTAATTCTTGGATGACCCa  <  2:209221/141‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                         
TCTTCATCACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGATTACCCA  >  USA300TCH1516_ALE/973077‑973350

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑