Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,788,621 G→A 33.8% pseudogene (2227/2253 nt) ygaQ → uncharacterized protein, putative enzyme

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,788,6210GA33.8% 18.5 / 3.9 26pseudogene (2227/2253 nt)ygaQuncharacterized protein, putative enzyme
Reads supporting (aligned to +/- strand):  ref base G (10/7);  new base A (2/7);  total (12/14)
Fisher's exact test for biased strand distribution p-value = 1.10e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

ACTCTCCTCATGATGGACTAGTTATAATAAATAAAGGAAACGAAGAAGTTGAAGGTACCTGGCCTAACAAATTGCAACCTGGAATATACAAAAACATGGGGAGTAATAGCGTTAACATTATTATTAATAATACCCGAAAAATTATCCCCCCTGGTAAAGTATTTACGCTTAGAGGCGGAACTCTAAATAT‑CAATATTCCTGGGCGT‑AGCGCTCTTCTTTTAGGG‑AAAACA‑GGAGAACCGCCGAACTATCTCTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGATAATATGTTTAGTTTACTAACGGTCATTTTGCAGTGAAGCCATTTACTGTTTTTTATCGACCAGATAATCTGTTCTCTAATGTTAACTCCCCCTAACCTGTTGCTTTAGTTATTCATTTCCTGTCTCACTTTGCCTTAATACCCTACGTTAAATGTTAC  >  NC_000913/2788388‑2788842
                                                                                                                                                                                                                                             |                                                                                                                                                                                                                             
cctccCCTAATGATGGACTAGTTATAAAAAATAAAGGAAACGAAGAAGTTGAAGGTACCTGGCCTAACAATTTGCAACCGGGAATATACAAAAACATGGGGAGTAATAGCGTTAACATTATTATTAATAATACCCGAAAAATTATCCCCCCTGGTAAAGTATTTACGCTTAGAGGCGGAACTCTAAATAT‑CAATATTCCTGGGCGT‑AGCGCTCTTCTTTTAGGG‑AAAACA‑GGAGAAccg                                                                                                                                                                                                                          <  1:167957/238‑1 (MQ=255)
         atgatgGACTAGTTATAATAAATAAAGGAAACGAAGAAGTTGAAGGTACCTGGCCTAACAAATTGCAACCTGGAATATACAAAAACATGGGGAGTAATAGCGTTAACATTATTATTAATAATACCCGAAAAATTATCCCCCCTGGTAAAGTATTTACGCTTAGAGGCGGAACACTAAATAT‑CAATATTCCTGGGCGT‑AGCGCTCTTCTTTTAGGG‑AAAAAA‑AGAGAAAAGCCGaaaaa                                                                                                                                                                                                                  >  2:167957/1‑235 (MQ=255)
           agggacagaGTTAAAAAAAATAAAGGAAACTAAGAGGTGGAAGGTACCGGGCCGAAAAAATTCAAACTTGAAATATACAAAAACATGGGGAGTAATAGCTTTAACTTTATTATTAATAATGCCCGAAAAATTATCCCCCATGGTAAATTTTTTCCTCTTAGAGGTGGAACTCTAAATAT‑CAATATTCCTGGCCGG‑AGGCTTCTTTTTTTAGGG‑AAAACA‑GGAGAACCGCCGAACTAtct                                                                                                                                                                                                               <  1:316917/231‑1 (MQ=255)
              ggACTAGTTATAATAAATAAAGGAAACGAAGAAGTTGAAGGTACCTGGCCTAACAAATTGCAACCTGGAATATACAAAAACATGGGGAGTAATAGCGTTAACATTATTATTAATAATACCCGAAAAATTATCCCCCCTGGTAAAGTATTTACGCTTAGAGGCGGAACTCTAAATAT‑TAATATTCCTGGGGGT‑AACGCTCTTCTTTTAGGG‑GAAAAA‑GGAAAAACCCCGAAcattatcca                                                                                                                                                                                                            >  2:1267997/1‑231 (MQ=255)
                               taaaGGAAACGAAGAAGTTGAAGGTACCTGGCCTAACAAATTGCAACCTGGAATATACAAAAACATGGGGAGTAATAGCGTTAACATTATTATTAATAATACCCGAAAAATTATCCCCCCTGGTAAAGTATTTACGCTTAGAGGCGGAAATCTAAAAAT‑CAATATTCCTGGGCGT‑AACGCCCTTGTTTTTGGG‑AAAAAA‑GGAAAAACCCCGAACTATCCCTAATTTAAATTTAATGTta                                                                                                                                                                                           >  2:133375/1‑239 (MQ=255)
                                              agTTGAAGGTACCTGGCCTAACAAATTGCAACCTGGAATATACAAAAACATGGGGAGTAATAGCGTTAACATTATTATTAATAATACCCGAAAAATTATCCCCCCTGGTAAAGTATTTACGCTTAGAGGCGGAACTCTAAATAT‑CAATATTCCTTGGCGT‑AGCGCTCTTCTTTTAGGG‑GAAACA‑GGAGAACCCCCGAACTATCTCTCTTTTTAATTTAATTTTTTATTATCCCCCATaa                                                                                                                                                                            >  2:931904/1‑239 (MQ=255)
                                                                            aCCTGGAATATACAAAAACATGGGGAGTAATAGCGTTAACATTATTATTAATAATACCCGAAAAATTATCCCCCCTGGTAAAGTATTTACGCTTAGAGGCGGAACTCTAAATAT‑CAATATTCCTGGGCGG‑AACGCTCTTCTTTTAGGG‑AAAAAA‑GGAGAACCGCCGAACTATCTCTATTTATAATTTATTGTTATATCTGCCCCGATAAAACGGGGCACGTAATATTTTTAGTTTTCTa                                                                                                                                              >  1:1244157/1‑239 (MQ=255)
                                                                                                              gTTAACATTATTATTAATAATACCCGAAAAATTATCCCCCCTGGTAAAGTATTTACGCTTAGAGGCGGAACTCTAAATAT‑CAATATTCCTGGGCGT‑AGCGCTCTTCTTTTAGGG‑AAAACA‑GGAGAACCGCCGCACTATCTCTATTTTTAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGATAATATTTTTAGTTTTCTAACGGTCATTTTCACATGGAACCATTTATTGtttt                                                                                                            >  2:601150/1‑239 (MQ=255)
                                                                                                                      aattattaATAATACCCGAAAAATTACCCCCCCGGGTAAAGTATTTACGCTTAGAGGCGGAACTCTAAATAT‑AAATATTCCTGGGCGT‑AGCGTTCTTCTTTTAGGG‑AAAACA‑GGAAAACCGCCGAACTATCTCTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGATAATATGTTTAGTTTACTAACGGTCATTTTGCAGTGAAGCCATTTACTGTTTTTTATCGAc                                                                                                    <  1:931904/238‑1 (MQ=255)
                                                                                                                       attattaATAATACCCGAAAAATTATCCCCCCTGGTAAAGTATTTACGCTTAGAGGCGGAACTCTAAATAT‑CAATATTCCTGGGCGT‑AGCGCTCTTCTTTTAGGG‑AAAACA‑GGAGAACCGCCGAACTATCTCTATTTATAATTTAATGTTATATCTGCCCCGCTAAAACGGGGCCGATAATATGTTTAGTTTACTAACGGTCATTTTTCAGTGAAGCCATTTAATGTTTTTTATCGaac                                                                                                   >  2:219178/1‑237 (MQ=255)
                                                                                                                                 atccccGAAAAATTTCCCCCCCTGGTAAATTATTTACGTTTAGAGGCGGAACTCAAAATAG‑CAATATTCCTGGGCGT‑AGCGCTTTTTTTTTAGGG‑AAAACA‑GGAAAACCGCCGAACTATCTCTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGATAATATGTTTAGTTTACTAACGGTCATTTTGCAGTGAAGCCATTTACTGTTTTTTATCGACCAGATAATCTg                                                                                         <  1:1279458/236‑1 (MQ=255)
                                                                                                                                 ataCCCAAAAATTTTCCCCCCCTAGAAAATTTTTATCTTTTGGAGGCGG‑ATTCAAAAAATACAATATT‑CGGGGCGTGAGC‑CTTTTTTTTTGGGGAAAAAAA‑GGGAAACCGCCGAACTATCTCTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGATAATATGTTTAGTTTACTAACGGTCATTTTGCAGTGAAGCCATTTACTGTTTTTTATCGACCAGATAATCTg                                                                                         <  2:1244157/239‑1 (MQ=255)
                                                                                                                                  taCCCGAAAAATTATCCCCCCTGGTAAAGTATTTACGCTTAGAGGCGGAACTCTAAATAT‑CAATATTCCTGGGCGT‑AGCGCTCTTCTTTTAGGG‑CAAACA‑GGAGAACCGCCGAACTATCTCTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGATAATATGTTTAGTTTACTAACGGTCATTTTGCAGTGAAGCCATTTACTGTTTTTTATTGACCAGCTaactttt                                                                                        >  1:496736/1‑234 (MQ=255)
                                                                                                                                  taCCCGAAAAATTATCCCCCCTGGTAAAGTATTTACGCTTAGAGGCGGAACTCTAAATAT‑CAATATTCCTGGGCGT‑AGCGCTCTTCTTTTAGGG‑AAAACA‑GGAGAACCGCCGAACTATCTCTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGGTAATATGTTTAGTTTACTAACGGCCATTTTGCAGGGAAACCCTTTCATGTTTTTTTTTGACCAGaaaaattgt                                                                                        >  2:1214509/1‑234 (MQ=255)
                                                                                                                                  taCCCGAAAAATTATCCCCCCTGGTAAAGTATTTACGCTTAGAGGCGGAACTCTAAATAT‑CAATATTCCTGGGCGT‑AGCGCTCTTCTTTTAGGG‑AAAACA‑GGAGAACCGCCGAAATTTCTCTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGGTAAAATGTTTAGTTTATACACGGGCATTTTTCAGTATAGACATTTAACGTTTTTTATCCACCAGATaaattgt                                                                                        >  2:1227870/1‑234 (MQ=255)
                                                                                                                                       ggaaatTTATCCCCCTGGGTAAAGTATTTACGCTTAGAGGCGGAACTATAAATAT‑CAATTGTCCTGCGCGT‑AGCGCTTTTATTTTAGGG‑AAAACA‑GGAGAACCGCCGAACTATCTCTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGATAATATGTTTAGTTTACTAACGGTCATTTTGCAGTGAAGCCATTTACTGTTTTTTATCGACCAGATAATCTGTTctct                                                                                   <  1:409903/237‑1 (MQ=255)
                                                                                                                                                     ccTTGTAAAGTATTTACGGTTAGGGGGAGAACTTTAAATAA‑CAATATTCCTGGGCGT‑AGCTCTCTTCTTTTAGGG‑AAAACA‑GGAGAACCGCCGAACTATCTCTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGATAATATGTTTAGTTTACTAACGGTCATTTTGCAGTGAAGCCATTTACTGTTTTTTATCGACCAGATAATCTGTTCTCTAATGTTAACTcccc                                                                     <  1:1227870/239‑1 (MQ=255)
                                                                                                                                                     ccTGGAAAAGTATTTACGTTGAGAGGCGGAACTCAAAATTA‑CAATATCCCGGGGCGT‑AGCGTTTTTTTTTTAGGA‑AAAAAA‑GGAGAACCGCCGAACTATCTCTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGATAATATGTTTAGTTTACTAACGGTCATTTTGCAGTGAAGCCATTTACTGTTTTTTATCGACCAGATAATCTGTTCTCTAATGTTAACTcccc                                                                     <  1:601150/239‑1 (MQ=255)
                                                                                                                                                            aaGTATTTGCGCTTAGGGGCGGAACTTAAAATAT‑AAATATTCCTGGGCTT‑AGCGCTTTTTTTTAAGGA‑AAAACA‑GGAAAACCGCCGAACTATCTCTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGATAATATGTTTAGTTTACTAACGGTCATTTTGCAGTGAAGCCATTTACTGTTTTTTATCGACCAGATAATCTGTTCTCTAATGTTAACTCCCCCTAACCt                                                              <  1:1010133/239‑1 (MQ=255)
                                                                                                                                                                                gaaatgaaaaaTAT‑AAATTTGCGGGGGTGT‑GGCGCTCTTTTTTTAGAG‑AAACCG‑GGAGAACCGCCGAACTATCTCTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGATAATATGTTTAGTTTACTAACGGTCATTTTGCAGTGAAGCCATTTACTGTTTTTTATCGACCAGATAATCTGTTCTCTAATGTTAACTCCCCCTAACCTGTTGCTTTAGTTATTCAtt                                           <  2:267669/230‑1 (MQ=255)
                                                                                                                                                                                            at‑CAATATTCCTGGGCGT‑AGCTATCTTCTTTTAGGA‑AAAACA‑GGAGAACCGCCGAACTATCTCTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGATAATATGTTTAGTTTACTAACGGTCATTTTGCAGTGAAGCCATTTACTGTTTTTTATCGACCAGATAATCTGTTCTCTAATGTTAACTCCCCCTAACCTGTTGCTTTAGTTATTCATTTCCTGTCTCACtt                              <  1:1267997/239‑1 (MQ=255)
                                                                                                                                                                                            at‑CAATATTCCGGGGCGT‑AGCGCTCTTCTTTTAGGA‑AAAACA‑GGAAAACCGCCGAACTATCTCTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGATAATATGTTTAGTTTACTAACGGTCATTTTGCAGTGAAGCCATTTACTGTTTTTTATCGACCAGATAATCTGTTCTCTAATGTTAACTCCCCCTAACCTGTTGCTTTAGTTATTCATTTCCTGTCTCACtt                              <  1:1214509/239‑1 (MQ=255)
                                                                                                                                                                                               cAATATTCCTGGGCGT‑AGCGCTCTTCTTTTAGGG‑AAAACA‑GGAGAACCGCCGAACTATCTCTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGATAATATGTTTAGTTTACTAACGGTCATTTTGCAGTGAAGCCATTTACTGTTTTTTATCGACCAGATAATCTGTTCTCTAATGTTAACTCCCCCTAACCTGTTGCTTTAGTTATTCATTTCCTGTCTCACttt                             >  1:12207/1‑238 (MQ=255)
                                                                                                                                                                                                      tcttggggttggcttttttttttgAGAG‑AAACAA‑GGAAAACCGCCGAACTATCTCTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGATAATATGTTTAGTTTACTAACGGTCATTTTGCAGTGAAGCCATTTACTGTTTTTTATCGACCAGATAATCTGTTCTCTAATGTTAACTCCCCCTAACCTGTTGCTTTAGTTATTCATTTCCTGTCTCACTTTGCCTTaa                      <  2:496736/219‑1 (MQ=255)
                                                                                                                                                                                                              t‑AGCGCTCTTCTTTTAGGG‑AAAACA‑GGAGAACCGCCGAACTATCTCTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGATAATATGTTTAGTTTACTAACGGTCATTTTGCAGTGAAGCCATTTACTGTTTTTTATCGACCAGATAATCTGTTCTCTAATGTTAA‑‑‑CCCCTAACCTGTTGCTTTAGTTATTCATTTCCTGTCTCACTTTGCCTTAATACCCTACGTTa          >  1:715726/1‑239 (MQ=255)
                                                                                                                                                                                                                        ttttttttgg‑AAAACGGGGAAAACCGCCGAACTATCTTTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGATAATATGTTTAGTTTACTAACGGTCATTTTGCAGTGAAGCCATTTACTGTTTTTTATCGACCAGATAATCTGTTCTCTAATGTTAA‑‑‑CCCCTAACCTGTTGCTTTAGTTATTCATTTCCTGTCTCACTTTGCCTTAATACCCTACGTTAAATGTTAc  <  2:715726/231‑1 (MQ=255)
                                                                                                                                                                                                                                             |                                                                                                                                                                                                                             
ACTCTCCTCATGATGGACTAGTTATAATAAATAAAGGAAACGAAGAAGTTGAAGGTACCTGGCCTAACAAATTGCAACCTGGAATATACAAAAACATGGGGAGTAATAGCGTTAACATTATTATTAATAATACCCGAAAAATTATCCCCCCTGGTAAAGTATTTACGCTTAGAGGCGGAACTCTAAATAT‑CAATATTCCTGGGCGT‑AGCGCTCTTCTTTTAGGG‑AAAACA‑GGAGAACCGCCGAACTATCTCTATTTATAATTTAATGTTATATCTGCCCCGATAAAACGGGGCAGATAATATGTTTAGTTTACTAACGGTCATTTTGCAGTGAAGCCATTTACTGTTTTTTATCGACCAGATAATCTGTTCTCTAATGTTAACTCCCCCTAACCTGTTGCTTTAGTTATTCATTTCCTGTCTCACTTTGCCTTAATACCCTACGTTAAATGTTAC  >  NC_000913/2788388‑2788842

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑