Predicted mutation
evidence seq id position mutation freq annotation gene description
RA KT2440 4,291,840 T→G 27.9% intergenic (‑142/‑20) sdhL ← / → CJ019_04025 Shikimate dehydrogenase‑like protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*KT24404,291,8400TG27.9% 73.6 / 4.6 52intergenic (‑142/‑20)sdhL/CJ019_04025Shikimate dehydrogenase‑like protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (9/27);  new base G (14/2);  total (23/29)
Fisher's exact test for biased strand distribution p-value = 4.00e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTGAAACGTTTATTCAGCGTAACAGAGTCAGCCACTGGTCGTCCCTTACACAACCTTTACCGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATGGGCATGGTGGTTGGTATGGGCCGG  >  KT2440/4291718‑4291974
                                                                                                                          |                                                                                                                                      
aCTGAAACGTTTATTCAGCGTAACAGAGTCAGCCACTGGTCGTCCCTTACACAACCTTTACCGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGGTTTGCGGCGAgg                                                                                                                            >  5:109503/1‑135 (MQ=255)
       cGTTTATTCAGCGTAACAGAGTCAGCCACTGGTCGTCCCTTACACAACCTTGACCGTTCCCCTGTGCTCAGCTGACAGCGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGGTTTCCGGCGGGGGTGtgtt                                                                                                                     >  2:158239/1‑135 (MQ=255)
       cGTTTATTCAGCGTAACAGAGTCAGCCACTGGTCGTCCATTACACAACCTTTACCGTTCCCCTGGGGGCAGCTGACAGCCGCCGGAGTCATAGTAACAGGGCGCCGGACGGGGGGGTCTACTGCGAGGGTGtttt                                                                                                                     >  8:137464/1‑135 (MQ=255)
          ttATTCAGCGTAACAGAGTCAGCCACTGGTCGTCCCTTACACAACCTTTACCGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATg                                                                                                                  <  5:138790/135‑1 (MQ=255)
                          agTCAGCCACTGGTCGTCCCTTACACAACCTTTACCGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCg                                                                                                  <  6:116522/135‑1 (MQ=255)
                               gCCACTGGTCGTCCCTTACACAACCTTTACCGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATc                                                                                             <  3:21116/135‑1 (MQ=255)
                                  aCTGGTCGTCCCTTACACAACCTTTACCGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCTGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTc                                                                                          <  5:54199/135‑1 (MQ=255)
                                    tGGTCGTCCCTTACACAACCTTTACCGTTCCCCTGTGCTCAGCTGAGAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCct                                                                                        <  5:41001/135‑1 (MQ=255)
                                       tcgtcCCTTACACAACCTTTACCGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCctgct                                                                                     <  7:79873/135‑1 (MQ=255)
                                        cgtcCCTTACACAACCTTTACCGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCctgctg                                                                                    <  1:242135/135‑1 (MQ=255)
                                             cTTACACAACCTTTACCGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGTTTTACTGGGAGGTTGTTTTATGTACCGGCTCATTACCGGAATAGTCCTGCTGGTCgg                                                                               >  2:242135/1‑135 (MQ=255)
                                             cTTACACAACCTTTACCGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGGTTTGCTGCGAGGTTGTTTTTTTAACCGTGTCAATCCCGGAATCGTCCTGCTGGTggg                                                                               >  7:35778/1‑135 (MQ=255)
                                             cTTACACAACCTTTACCGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGGTTTCCGGCGCGGTTGTTTTATGAACCGGCTCCTTACCGGCATCGTCCTGCTGGGCgg                                                                               >  7:184072/1‑135 (MQ=255)
                                              ttACACAACCTTTACCGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGt                                                                              <  7:283581/135‑1 (MQ=255)
                                                         ttACCGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGGTTTGCTGCGAGGGTGTTTTTTTATACGGCTCATTACCCGAATCGTCCAGCGGGTCGGTGCCCTGGccct                                                                   >  2:28931/1‑133 (MQ=255)
                                                         ttACCGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGGTTTACTGCGAGGTTGTTTTTTTAACCCTCTGCTTACCGGAATCGTCCGGCGGGTCGGTGCCCTGGCCag                                                                   >  2:22331/1‑134 (MQ=255)
                                                         ttACCGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGGTTTAATGGGAGGTTTTTTTATTAACCGTATCATTCCCGAAAAAGGCCTGCAGGTCTGTGgccactcca                                                                    >  4:56739/1‑128 (MQ=255)
                                                           aCCGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCAt                                                                   <  7:1896/133‑1 (MQ=255)
                                                           aCCGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCATc                                                                  <  1:22331/134‑1 (MQ=255)
                                                            ccGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGGTTTACTGCGAGGTTGTTTTTTGAACCGTCTCATTCCCGGAATAGTCCTGCTGGTGGGTGCCCTGGCCAACAg                                                                >  8:283581/1‑135 (MQ=255)
                                                             cGTTCCCCTGTTCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCATCAg                                                                <  3:56739/134‑1 (MQ=255)
                                                              gTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGTTTTACTGCGAGGTTTTTTTATGAACCGGCACATTACCGGAATCGTCCTGCTGGTGGGTGCCCAGGCCCTCAACg                                                              >  4:187450/1‑135 (MQ=255)
                                                                   ccTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGGTTTGCTGGGAGGTTGTTTTTTGAAACGTCTCATTACCGGAATCGTCCTGCTGGTCGGTGCCCTGGGCCGAAGCGGGCCt                                                         >  8:1896/1‑135 (MQ=255)
                                                                   ccTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGGGTTGCTGCGCGGTTGTTTTTTGTAACGTCTGCTTACCCGGAGCGTCCTGCTGGTGGGTGGCCGGGCCCTGCGCGGGCCt                                                         >  1:274346/1‑135 (MQ=255)
                                                                    cTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGTTTTACTGCGCGGTTGTTTTTTGAACCGGCTCATTACGCGCCTCGTCCTGCTGGTCGGTGCCCTGGCCCTCACCGGGccgg                                                        >  3:122389/1‑133 (MQ=255)
                                                                       tgCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGTTTTGCTGGGAGGTTGTTTTTTGTTCCGTCTCATTACCGGGATAGTCCGGCTGGTGGGTGGCCGGGCCCTCGGCGGGCGGgcag                                                     >  2:243825/1‑135 (MQ=255)
                                                                       tgCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGGTTTGGTGCGAGGTTGTTTTTTTAACCGTGTCATTGCCGGAATCGTCCTGCTGGTCGGTGGCCTGGGCCTCAGCGGGCCGgcag                                                     >  2:239868/1‑135 (MQ=255)
                                                                       tgCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGGTTTGCTGCGAGGTTGTTTTTTTAAACCGCTCATTACCGGAATAGTCCAGCTGGGCGGTGGCCTGGCCCTCAGCGGGCCGgccg                                                     >  7:136838/1‑133 (MQ=255)
                                                                          tCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGTTTTGCTGCGTGGTTGTTTTATTAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCAGGGCCTCAGCGGGCCTGccgcag                                                  >  7:20977/1‑135 (MQ=255)
                                                                                           gAGTCATAGTAACAGGGCCCCGGACGTGGGGTTGTCCTGAGAGGTTGTTTTATTGCCCGTCACAATCCCCGAATCCTCCGGCTGGTCGGTGCCCGGGCCATCAGCGGGCCTTCAGCCGCGCACCCCCGCTATgtc                                 >  8:65324/1‑133 (MQ=255)
                                                                                                 tAGTAACAGGGCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTCTGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCAt                           <  7:236656/135‑1 (MQ=255)
                                                                                                 tAGTAACAGGGCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCAt                           <  3:280140/135‑1 (MQ=255)
                                                                                                    tAACAGGGCCCCGGACGTGGGGTTTTCCTGGGAGGTTGTTTTATTAAACGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCATCAGCGGGCCTGCAGCCGCGCACGGCGGGTATGGCGGCCAttg                         >  8:162386/1‑132 (MQ=255)
                                                                                                    tAACAGGGCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATggg                        >  8:166902/1‑135 (MQ=255)
                                                                                                     aaCAGGGCCCCGGACGTGGTGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATGGGc                       <  6:135211/135‑1 (MQ=255)
                                                                                                     aaCAGGGCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATGGGc                       <  7:160365/135‑1 (MQ=255)
                                                                                                         gggCCCCGGACGTGGGGTTTTGCTGCGAGGTTGTTTTATGAACCGTGTCATTACCGGAATAGTCCTGCTGGTAGGTGCCCTGGCCATCAGCGGGCCTGCCGCAGCGCCCGGCGGCGATTGCGGgcatgggcatgg                   >  4:126721/1‑135 (MQ=255)
                                                                                                         gggCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATGGGCAtgg                   <  1:227314/135‑1 (MQ=255)
                                                                                                         gggCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATGGGCAtgg                   <  4:93874/135‑1 (MQ=255)
                                                                                                          gggcgcGGACGTGGGGTGTTCCTGCGCGGTTGTTTTATGAACCGGCTCATTCCCGGACTCGTGCTGCTTGTCGGTGCCCTGGCCATCAGCGGGGCTGGAGCATCGGAGGGGGGCTATGGCGGCCATGGGCAtggt                  <  6:99084/130‑1 (MQ=255)
                                                                                                          ggCCCCGGTCGTGGTGTGTTCCTGCGAGGGTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATGGGCAtggt                  <  2:117473/135‑1 (MQ=255)
                                                                                                          ggCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATGGGCAtggt                  <  8:273650/135‑1 (MQ=255)
                                                                                                          ggCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATGGGCAtggt                  <  8:35778/135‑1 (MQ=255)
                                                                                                               cGGAGGTGGGGGTTTCCTGCGAGGTTGTGTTATGAACCGTCTCATTCCCGGACTCGTCCTGCTGGGCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATGGGCATGGtggttg             <  5:239002/135‑1 (MQ=255)
                                                                                                               cGGACTTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCGGGGTATCGTCCTGCTGGTCGGTGCCCTGGGCATCAGCGGGCCTGCAGCAGCGCACGTCGGCTATGGCGGCTATGGGCATGGtggttg             <  8:137942/135‑1 (MQ=255)
                                                                                                               cGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGGCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATGGGCATGGtggttg             <  7:31923/135‑1 (MQ=255)
                                                                                                               cGGACGTGGGGGTTTGCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTTCCCTGGGCAACACCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCAAGGGGATGGtggttg             >  8:70895/1‑135 (MQ=255)
                                                                                                               cGGACGTGGGGGGTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGTCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATGGGCATGGtggttg             <  4:125747/135‑1 (MQ=255)
                                                                                                                ggccGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGGCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATGGGCATGGtggttgg            <  7:286876/132‑1 (MQ=255)
                                                                                                                         gTTTTCCTGCGATGTTGTTTTATGAACCGTCTCATTCCCGGACTCGTCCTGCTGGTCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATGGGCATGGTGGTTGGTATGGGCCg   <  7:70123/135‑1 (MQ=255)
                                                                                                                         gTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATGGGCATGGTGGTTGGTATGGGCCg   <  1:28931/135‑1 (MQ=255)
                                                                                                                         gTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGGCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATGGGCATGGTGGTTGGTATGGGCCg   <  7:16711/135‑1 (MQ=255)
                                                                                                                          ttttCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATGGGCATGGTGGTTGGTATGGGCCgg  <  3:88461/135‑1 (MQ=255)
                                                                                                                          ttttCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATGGGCATGGTGGTTGGTATGGGCCgg  <  8:20977/135‑1 (MQ=255)
                                                                                                                          |                                                                                                                                      
ACTGAAACGTTTATTCAGCGTAACAGAGTCAGCCACTGGTCGTCCCTTACACAACCTTTACCGTTCCCCTGTGCTCAGCTGACAGAGGCCGGAGTCATAGTAACAGGGCCCCGGACGTGGGGTTTTCCTGCGAGGTTGTTTTATGAACCGTCTCATTCCCGGAATCGTCCTGCTGGTCGGTGCCCTGGCCATCAGCGGGCCTGCAGCAGCGCACGGCGGCTATGGCGGCCATGGGCATGGTGGTTGGTATGGGCCGG  >  KT2440/4291718‑4291974

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑