Predicted mutation
evidence seq id position mutation freq annotation gene description
RA AP009048 406,395 C→T 13.5% intergenic (+1/‑257) yaiA → / → aroM hypothetical protein/conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AP009048406,3950CT13.5% 160.9 / 14.5 59intergenic (+1/‑257)yaiA/aroMhypothetical protein/conserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (24/27);  new base T (5/3);  total (29/30)
Fisher's exact test for biased strand distribution p-value = 4.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.26e-01

AGTGAACATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACATTTTTCATAAT  >  AP009048/406326‑406462
                                                                     |                                                                   
aGTGAACATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGAcc                                                                    >  1:2203273/1‑71 (MQ=255)
aGTGAACATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGAcc                                                                    <  1:1489116/71‑1 (MQ=255)
  tGAACATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCg                                                                   >  1:3340552/1‑70 (MQ=255)
   gAACATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCa                                                                 >  1:54380/1‑71 (MQ=255)
    aaCATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCAt                                                                <  1:498175/71‑1 (MQ=255)
     aCATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCAt                                                                <  1:763505/70‑1 (MQ=255)
      cATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGATCGCATCa                                                              <  1:2948472/71‑1 (MQ=255)
        tCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGATCGCATCAGa                                                            >  1:408586/1‑71 (MQ=255)
             ccGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGCCCGCATCAGa                                                            >  1:554242/1‑66 (MQ=255)
                cTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCgg                                                    <  1:3035041/71‑1 (MQ=255)
                cTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCg                                                     >  1:4593856/1‑70 (MQ=255)
                 tCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCgg                                                    >  1:470089/1‑70 (MQ=255)
                 tCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCgg                                                    >  1:4530151/1‑70 (MQ=255)
                  cAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCgg                                                    >  1:3480324/1‑69 (MQ=255)
                  cAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCgg                                                    >  1:2778385/1‑69 (MQ=255)
                   aGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCgg                                                    <  1:1780585/68‑1 (MQ=255)
                   aGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGa                                                   <  1:3821739/69‑1 (MQ=255)
                         cGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTc                                           <  1:537850/71‑1 (MQ=255)
                          gatggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCgg                                                    <  1:4492319/61‑1 (MQ=255)
                          gatggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCt                                          <  1:4124598/71‑1 (MQ=255)
                           atggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCa                                                                 <  1:3820773/47‑1 (MQ=255)
                            tggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGATCGCATCAGACTGCTCGGAAGGGATTCt                                          >  1:2959678/1‑69 (MQ=255)
                            tggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGa                                        <  1:2784589/71‑1 (MQ=255)
                             ggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAgg                                                <  1:4589952/62‑1 (MQ=255)
                                tgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGAtt                                            <  1:2166253/63‑1 (MQ=255)
                                tgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCt                                          <  1:307551/65‑1 (MQ=255)
                                  cGAAAAAACGCTATGAGGACCCTGACAAAGAGTGATCGCATCAGAc                                                           >  1:1221863/1‑46 (MQ=255)
                                  cGAAAAAACGCTATGAGGACCCTGACAAAGAGTGATCGCATCAGAc                                                           >  1:983427/1‑46 (MQ=255)
                                  cGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCa                                  >  1:1345243/1‑71 (MQ=255)
                                   gAAAAAACGCTATGAGGACCCTGACAAAGAGTGATCGCATCAGACTGCTCCGAAGGGATTCTGAGTGCCAc                                 >  1:167893/1‑71 (MQ=255)
                                   gAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCAc                                 >  1:1749690/1‑71 (MQ=255)
                                    aaaaaaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGa                                              >  1:3925801/1‑57 (MQ=255)
                                    aaaaaaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCt                                          <  1:3608934/61‑1 (MQ=255)
                                    aaaaaaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTg                                         <  1:3157016/62‑1 (MQ=255)
                                    aaaaaaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTg                                         <  1:470624/62‑1 (MQ=255)
                                    aaaaaaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCa                                  >  1:2674162/1‑69 (MQ=255)
                                    aaaaaaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACt                                <  1:219756/71‑1 (MQ=255)
                                     aaaaaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTa                               >  1:1291010/1‑71 (MQ=255)
                                     aaaaaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTa                               >  1:3129678/1‑71 (MQ=255)
                                     aaaaaCGCTATGAGGACCCTGAAAAAGAGTGACCGCATc                                                               >  1:3519500/1‑39 (MQ=255)
                                      aaaaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCa                                                              >  1:1476987/1‑39 (MQ=255)
                                        aaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACaa                            <  1:3265574/71‑1 (MQ=255)
                                         aCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCt                                          <  1:313006/56‑1 (MQ=255)
                                          cGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAgg                          >  1:390342/1‑71 (MQ=255)
                                           gCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAggg                         <  1:2098784/71‑1 (MQ=255)
                                             tATGAGGACCCTGACAAAGAGTGATCGCATCAGACTGCTCgg                                                    <  1:828657/42‑1 (MQ=255)
                                             tATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGAt                       >  1:295247/1‑71 (MQ=255)
                                             tATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGAt                       >  1:1531807/1‑71 (MQ=255)
                                               tGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCt                     <  1:852284/71‑1 (MQ=255)
                                                 aGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTg                    <  1:2666981/70‑1 (MQ=255)
                                                      ccTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTg                                         <  1:3382645/44‑1 (MQ=255)
                                                        tGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGAt                                             <  1:4587609/38‑1 (MQ=255)
                                                          aCAAAGAGTGACCGCATCAGACTGCTCGGAAGGGAtt                                            >  1:2913287/1‑37 (MQ=255)
                                                          aCAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTc                                           >  1:4030344/1‑38 (MQ=255)
                                                          aCAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACAttt          <  1:263794/71‑1 (MQ=255)
                                                          aCAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACAttt          <  1:2238962/71‑1 (MQ=255)
                                                          aCAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACAttt          >  1:2745365/1‑71 (MQ=255)
                                                          aCAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACAtt           <  1:2891058/70‑1 (MQ=255)
                                                            aaaGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATATGCGTCACAtttt         >  1:3272875/1‑70 (MQ=255)
                                                                agTGACCGCATCAGACTGCTCGGAAGGGATTCTGAg                                       >  1:1448400/1‑36 (MQ=255)
                                                                  tGATCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACATTTTTCATAAt  <  1:3572578/71‑1 (MQ=255)
                                                                     ccGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCg                  <  1:1963950/52‑1 (MQ=255)
                                                                     |                                                                   
AGTGAACATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACATTTTTCATAAT  >  AP009048/406326‑406462

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: