Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,885,984 C→T 32.9% intergenic (‑109/+250) ygcB ← / ← cysH conserved hypothetical protein, member of DEAD box family/3'‑phosphoadenosine 5'‑phosphosulfate reductase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,885,9840CT32.9% 104.7 / 74.4 85intergenic (‑109/+250)ygcB/cysHconserved hypothetical protein, member of DEAD box family/3'‑phosphoadenosine 5'‑phosphosulfate reductase
Reads supporting (aligned to +/- strand):  ref base C (38/19);  new base T (19/9);  total (57/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTTCGATGCTGCTCATAAATATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGATAGAAATATCG  >  W3110S.gb/2885925‑2886049
                                                           |                                                                 
ttttCGATGCTGCTCATAAATATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGTAAAGAAGAGAc                                                        >  1:1413120/1‑71 (MQ=255)
ttttCGATGCTGCTCATAAATATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGTAAAGAAGAGAc                                                        >  1:3072572/1‑71 (MQ=255)
 tttCGATGCTGCTCATAAATATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGTAAAGAAGAGAc                                                        >  1:982163/1‑70 (MQ=255)
 tttCGATGCTGCTCATAAATATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGTAAAGAAGAGAc                                                        >  1:1413259/1‑70 (MQ=255)
 tttCGATGCTGCTCATAAATATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGTAAAGAAGAGAc                                                        >  1:1804901/1‑70 (MQ=255)
 tttCGATGCTGCTCATAAATATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGTAAAGAAGAGAc                                                        >  1:1362117/1‑70 (MQ=255)
 tttCGATGCTGCTCATAAATATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGTAAAGAAGAGAc                                                        >  1:2344483/1‑70 (MQ=255)
 tttCGATGCTGCTCATAAATATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGTAAAGAAGAGAc                                                        >  1:2804047/1‑70 (MQ=255)
 tttCGATGCTGCTCATAAATATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGTAAAGAAGAGAc                                                        >  1:1204351/1‑70 (MQ=255)
 tttCGATGCTGCTCATAAATATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGTAAAGAAGAGAc                                                        >  1:3211146/1‑70 (MQ=255)
               aTAAATATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGCAAAGAAGAGACt                                                       <  1:2915508/57‑1 (MQ=255)
               aTAAATATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGCAAAGAAGAGACt                                                       <  1:2726968/57‑1 (MQ=255)
               aTAAATATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGCAAAGAAGAGACt                                                       <  1:1132510/57‑1 (MQ=255)
               aTAAATATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGCAAAGAAGAGACt                                                       <  1:1864687/57‑1 (MQ=255)
                 aaaTATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGCAAAGAAGAGAc                                                        >  1:2839916/1‑54 (MQ=255)
                 aaaTATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGCAAAGAAGAGACTaa                                                     >  1:1004437/1‑57 (MQ=255)
                 aaaTATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGCAAAGAAGAGACTaa                                                     >  1:647627/1‑57 (MQ=255)
                 aaaTATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGCAAAGAAGAGACTaa                                                     >  1:665385/1‑57 (MQ=255)
                 aaaTATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGCAAAGAAGAGACTaa                                                     >  1:2371136/1‑57 (MQ=255)
                 aaaTATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGCAAAGAAGAGACTaa                                                     >  1:1638037/1‑57 (MQ=255)
                 aaaTATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGCAAAGAAGAGACTaa                                                     >  1:1507601/1‑57 (MQ=255)
                 aaaTATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGCAAAGAAGAGACTaa                                                     >  1:1431882/1‑57 (MQ=255)
                 aaaTATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGCAAAGAAGAGACTaa                                                     >  1:1231448/1‑57 (MQ=255)
                 aaaTATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGCAAAGAAGAGACTaa                                                     >  1:1106334/1‑57 (MQ=255)
                 aaaTATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGCAAAGAAGAGACTaa                                                     >  1:1297627/1‑57 (MQ=255)
                 aaaTATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGCAAAGAAGAGAATaa                                                     >  1:2123534/1‑57 (MQ=255)
                 aaaTATCGAATTACAGTGATATACACATGTCTTGCCTCACTGCAAAGAAGAGACTa                                                      >  1:1429216/1‑56 (MQ=255)
                  aaTATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGTAAAGAAGAGACTAACATTCGAATTGTTTg                                      >  1:2979282/1‑71 (MQ=255)
                  aaTATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGTAAAGAAGAGACTAACATTCGAATTGTTTg                                      >  1:2919101/1‑71 (MQ=255)
                  aaTATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGTAAAGAAGAGACTAACATTCGAATTGTTTg                                      >  1:2697176/1‑71 (MQ=255)
                  aaTATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGTAAAGAAGAGACTAACATTCGAATTGTTTg                                      >  1:2084724/1‑71 (MQ=255)
                  aaTATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGTAAAGAAGAGACTAACATTCGAATTGTTTg                                      >  1:1318601/1‑71 (MQ=255)
                  aaTATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGTAAAGAAGAGACTAACATTCGAATTGTTTg                                      >  1:1413022/1‑71 (MQ=255)
                     atCGAATTACAGTGATATACACATGTCTTGCCTACCTGCAAAGAAGAGACTAACAt                                                  >  1:1958002/1‑56 (MQ=255)
                                   atatACACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGaa                              >  1:931223/1‑62 (MQ=255)
                                   atatACACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCt                     >  1:947504/1‑71 (MQ=255)
                                   atatACACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCt                     >  1:3114356/1‑71 (MQ=255)
                                   atatACACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCt                     >  1:1686487/1‑71 (MQ=255)
                                   atatACACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCt                     >  1:2653772/1‑71 (MQ=255)
                                   atatACACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCt                     >  1:2440714/1‑71 (MQ=255)
                                    tataCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCt                          <  1:407438/65‑1 (MQ=255)
                                    tataCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCt                          <  1:531057/65‑1 (MQ=255)
                                    tataCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCt                          <  1:264797/65‑1 (MQ=255)
                                    tataCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCt                          <  1:2639657/65‑1 (MQ=255)
                                    tataCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCt                          <  1:1699196/65‑1 (MQ=255)
                                    tataCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCt                          <  1:1766489/65‑1 (MQ=255)
                                    tataCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCt                          <  1:2300455/65‑1 (MQ=255)
                                    tataCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCt                          <  1:75811/65‑1 (MQ=255)
                                    tataCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCt                          <  1:1849997/65‑1 (MQ=255)
                                      taCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTgg                        >  1:1110680/1‑65 (MQ=255)
                                      taCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTgg                        >  1:3185525/1‑65 (MQ=255)
                                      taCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTgg                        >  1:1611910/1‑65 (MQ=255)
                                      taCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTgg                        >  1:3282496/1‑65 (MQ=255)
                                      taCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTgg                        >  1:558096/1‑65 (MQ=255)
                                      taCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTgg                        >  1:1094231/1‑65 (MQ=255)
                                      taCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTgg                        >  1:705162/1‑65 (MQ=255)
                                      taCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTgg                        >  1:712310/1‑65 (MQ=255)
                                      taCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTgg                        >  1:738132/1‑65 (MQ=255)
                                      taCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTgg                        >  1:860936/1‑65 (MQ=255)
                                      taCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTgg                        >  1:2921122/1‑65 (MQ=255)
                                      taCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTgg                        >  1:2071943/1‑65 (MQ=255)
                                      taCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTgg                        >  1:1232016/1‑65 (MQ=255)
                                      taCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTgg                        >  1:129401/1‑65 (MQ=255)
                                      taCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTgg                        >  1:2117949/1‑65 (MQ=255)
                                      taCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTgg                        >  1:2997315/1‑65 (MQ=255)
                                      taCACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTgg                        >  1:2286545/1‑65 (MQ=255)
                                        cacaTGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGt                >  1:793427/1‑71 (MQ=255)
                                              tCTTGCCTCCCTGTAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGa             >  1:112251/1‑68 (MQ=255)
                                              tCTTGCCTCCCTGTAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGa             >  1:1767772/1‑68 (MQ=255)
                                              tCTTGCCTCCCTGTAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGa             >  1:2120922/1‑68 (MQ=255)
                                                  gCCTCCCTGTAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGATAGa         <  1:1178421/68‑1 (MQ=255)
                                                  gCCTCCCTGTAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGATAGa         <  1:382212/68‑1 (MQ=255)
                                                  gCCTCCCTGTAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGATAGa         <  1:2606396/68‑1 (MQ=255)
                                                       ccTGTAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGATAGAAATATc   <  1:614252/69‑1 (MQ=255)
                                                       ccTGTAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGATAGAAATATc   <  1:1064453/69‑1 (MQ=255)
                                                       ccTGTAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGATAGAAATATc   <  1:2602941/69‑1 (MQ=255)
                                                       ccTGTAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGATAGAAATATc   <  1:2656667/69‑1 (MQ=255)
                                                       ccTGTAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGATAGAAATATc   <  1:2845314/69‑1 (MQ=255)
                                                       ccTGTAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGATAGAAATATc   <  1:3171697/69‑1 (MQ=255)
                                                       ccTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGATAGAAATATCg  <  1:1307672/70‑1 (MQ=255)
                                                       ccTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGATAGAAATATCg  <  1:2086657/70‑1 (MQ=255)
                                                       ccTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGATAGAAATATCg  <  1:778076/70‑1 (MQ=255)
                                                       ccTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGATAGAAATATCg  <  1:491249/70‑1 (MQ=255)
                                                       ccTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGATAGAAATATCg  <  1:1728720/70‑1 (MQ=255)
                                                       ccTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGATAGAAATATCg  <  1:3016130/70‑1 (MQ=255)
                                                           |                                                                 
TTTTCGATGCTGCTCATAAATATCGAATTACAGTGATATACACATGTCTTGCCTCCCTGCAAAGAAGAGACTAACATTCGAATTGTTTGGGTTCGAACGCTGGCCTCAGGTTGATAGAAATATCG  >  W3110S.gb/2885925‑2886049

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: