Predicted mutation
evidence seq id position mutation freq annotation gene description
RA AP009048 310,235 C→G 5.5% S109T (AGC→ACC)  ykgK ← predicted regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AP009048310,2350CG 5.5% 225.3 / 2.6 73S109T (AGC→ACC) ykgKpredicted regulator
Reads supporting (aligned to +/- strand):  ref base C (40/29);  new base G (2/2);  total (42/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.61e-01

ATTAATCACATAGACCAGTTCTTTTCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGCAATCAATACGACCTGTTTCCCCT  >  AP009048/310165‑310304
                                                                      |                                                                     
aTTAATCACATAGACCAGTTCTTTTCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGc                                                                       <  1:1641835/71‑1 (MQ=255)
 ttAATCACATAGACCAGTTCTTTTCTAATATCACGACTCAGTCCAGCTTATACCACGCCCCTAATATTGc                                                                       >  1:2869422/1‑70 (MQ=255)
   aaTCACATAGACCAGTTCTTTTCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTAt                                                                    >  1:2777421/1‑71 (MQ=255)
   aaTCACATAGACCAGTTCTTTTCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTAt                                                                    >  1:2267804/1‑71 (MQ=255)
     tCACATAGACCAGTTCTTTTCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTg                                                                  >  1:1248649/1‑71 (MQ=255)
      cacaTAGACCAGTTCTTTTCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTg                                                                  >  1:3310729/1‑70 (MQ=255)
        caTAGACCAGTTCTTTTCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTaa                                                               >  1:4491476/1‑71 (MQ=255)
            gACCAGTTCTTTTCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGt                                                                 >  1:3861509/1‑65 (MQ=255)
               cAGTTCTTTTCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGGTATTACAATAGCaa                                                         >  1:261985/1‑70 (MQ=38)
               cAGTTCTTTTCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGGTATTACAATAGCaa                                                         >  1:2974613/1‑70 (MQ=38)
               cAGTTCTTTTCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGt                                                                 <  1:2124346/62‑1 (MQ=255)
                 gTTCTTTTCTAATATCACGACTCAGTCCAGCGTATACCCCGCCCCTAATATTGCTATTGTAATACCaataa                                                      >  1:205000/1‑71 (MQ=255)
                 gTTCTTTTCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTACAATAGCAATatta                                                          <  1:228050/67‑4 (MQ=37)
                  ttCTTTTCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTa                                                                     <  1:1718434/55‑1 (MQ=255)
                  ttCTTTTCTAATATCACGACTCAGTACAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCaataat                                                     <  1:3902435/71‑1 (MQ=255)
                   tCTTTTCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGGTATTACAATAGCaatatt                                                     <  1:4985884/70‑3 (MQ=37)
                     ttttCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTg                                                  >  1:49582/1‑71 (MQ=255)
                       ttCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGc                                                 >  1:3874962/1‑70 (MQ=255)
                       ttCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGc                                                 >  1:516196/1‑70 (MQ=255)
                        tCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCt                                                <  1:336172/70‑1 (MQ=255)
                        tCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCt                                                >  1:3882736/1‑70 (MQ=255)
                           aaTATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAAt                                                              >  1:1267814/1‑53 (MQ=255)
                            atatCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGc                                           >  1:4591080/1‑71 (MQ=255)
                            atatCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGc                                           <  1:860670/71‑1 (MQ=255)
                             tatCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTa                                               >  1:4195050/1‑66 (MQ=255)
                             tatCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGcc                                          >  1:1534335/1‑71 (MQ=255)
                               tCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCct                                         <  1:2314014/70‑1 (MQ=255)
                                cACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGc                                           <  1:928798/67‑1 (MQ=255)
                                 aCGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTa                                               >  1:725471/1‑62 (MQ=255)
                                 aCGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTa                                               >  1:3055740/1‑62 (MQ=255)
                                 aCGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCctct                                       <  1:1560634/70‑1 (MQ=255)
                                 aCGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCctct                                       <  1:4619361/70‑1 (MQ=255)
                                 aCGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCctct                                       >  1:3899821/1‑70 (MQ=255)
                                 aCGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTg                                      <  1:4840925/71‑1 (MQ=255)
                                 aCGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTg                                      <  1:1867449/71‑1 (MQ=255)
                                  cGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGa                                     >  1:2941278/1‑71 (MQ=255)
                                  cGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGa                                     <  1:1053/71‑1 (MQ=255)
                                   gACTCAGTCCAGCGTATACCACGCCCCTAATATTGGTATTACAATAGCaata                                                       <  1:3572687/52‑1 (MQ=25)
                                   gACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCaata                                                       <  1:853048/52‑1 (MQ=255)
                                   gACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCaata                                                       <  1:4258857/52‑1 (MQ=255)
                                   gACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGAc                                    >  1:4782534/1‑71 (MQ=255)
                                    aCTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACt                                   <  1:3047152/71‑1 (MQ=255)
                                     cTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCaataat                                                     >  1:4222594/1‑52 (MQ=255)
                                     cTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAAtt                                                    <  1:339154/53‑1 (MQ=255)
                                       cAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAAtt                                                    <  1:1375920/51‑1 (MQ=255)
                                        aGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACttt                                 <  1:4599578/69‑1 (MQ=255)
                                        aGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCt                               <  1:4584237/71‑1 (MQ=255)
                                        aGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCt                               >  1:1044814/1‑71 (MQ=255)
                                        aGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCt                               <  1:602454/71‑1 (MQ=255)
                                         gTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTg                              >  1:2742339/1‑71 (MQ=255)
                                              gCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTg                                                  >  1:1020928/1‑46 (MQ=255)
                                              gCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCg                          >  1:4215741/1‑70 (MQ=255)
                                              gCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCg                          >  1:4209868/1‑70 (MQ=255)
                                                 tataCCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCctct                                       <  1:2093823/54‑1 (MQ=255)
                                                  ataCCACGCCCCTAATATTGCTATTGTAATACAAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGcaat                      >  1:299219/1‑70 (MQ=255)
                                                    aCCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGcaatcaa                   >  1:5033890/1‑71 (MQ=255)
                                                    aCCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTATCTGGCCGcaatcaa                   >  1:5035708/1‑71 (MQ=255)
                                                     ccACGCCCCTAATATTGCTATTGTAATACCAATAATTTGc                                                 >  1:76242/1‑40 (MQ=255)
                                                     ccACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGcc                           >  1:3650943/1‑62 (MQ=255)
                                                     ccACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGcaatcaa                   <  1:825437/70‑1 (MQ=255)
                                                      cACGCCCCTAATATTGCTATTGTAATACCAATAAttt                                                   >  1:464915/1‑37 (MQ=255)
                                                      cACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGcaatcaa                   <  1:531840/69‑1 (MQ=255)
                                                        cGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGcaa                       >  1:3449123/1‑63 (MQ=255)
                                                         gCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGCAATCAATACg               <  1:1612807/70‑1 (MQ=255)
                                                         gCCCCAAATATTGCTATTGTAATACCAATAATTTGCTaa                                              >  1:3860585/1‑39 (MQ=255)
                                                          ccccTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCt                               >  1:3732301/1‑53 (MQ=255)
                                                          ccccTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGc                         <  1:1105508/59‑1 (MQ=255)
                                                             cTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGcaatcaa                   <  1:2746713/62‑1 (MQ=255)
                                                              tAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGcaatca                    <  1:4231782/60‑1 (MQ=255)
                                                              tAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGCAATCAATACGACCTGt         >  1:2068629/1‑71 (MQ=255)
                                                               aaTATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGCAATCAATACGACCTGtt        >  1:3393354/1‑71 (MQ=255)
                                                                atatTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGCAATCAATACGAc             >  1:3719711/1‑65 (MQ=255)
                                                                atatTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGCAATCAATACGACCTGttt       >  1:3832858/1‑71 (MQ=255)
                                                                atatTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGCAATCAATACGACCTGtt        <  1:2644081/70‑1 (MQ=255)
                                                                 tatTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGCAATCAATACGACCTGTTTc      >  1:2471587/1‑71 (MQ=255)
                                                                      cTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGCAATCAATACGACCTGTTTCCCCt  <  1:3211647/70‑1 (MQ=255)
                                                                      cTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGCAATCAATACGACCTGTTTCCCCt  <  1:1000158/70‑1 (MQ=255)
                                                                      |                                                                     
ATTAATCACATAGACCAGTTCTTTTCTAATATCACGACTCAGTCCAGCGTATACCACGCCCCTAATATTGCTATTGTAATACCAATAATTTGCTAAGGCCTCTGACTTTCTGGCCGCAATCAATACGACCTGTTTCCCCT  >  AP009048/310165‑310304

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑