Predicted mutation
evidence seq id position mutation freq annotation gene description
RA AP009048 4,165,968 T→A 5.5% T35T (ACT→ACA rpsL → 30S ribosomal subunit protein S12

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AP0090484,165,9680TA 5.5% 515.1 / 17.0 180T35T (ACT→ACArpsL30S ribosomal subunit protein S12
Reads supporting (aligned to +/- strand):  ref base T (79/91);  new base A (5/5);  total (84/96)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01

Only 100 of 184 total aligned reads displayed.

TGCTCGCAAAGTTGCGAAAAGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGTATGCCGTGTTCGTCTGACT  >  AP009048/4165899‑4166037
                                                                     |                                                                     
 gCTCGCAAAGTTGCGAAAAGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCg                                                                     >  1:7006714/1‑71 (MQ=255)
  cTCGCAAAGTTGCGAAAAGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCgt                                                                    <  1:7356481/71‑1 (MQ=255)
  cTCGCAAAGTTGCGAAAAGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCgt                                                                    >  1:4908565/1‑71 (MQ=255)
  cTCGCAAAGTTGCGAAAAGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCgt                                                                    <  1:7085720/71‑1 (MQ=255)
   tCGCAAAGTTGCGAAAAGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCgtg                                                                   >  1:2197301/1‑71 (MQ=255)
    cGCAAAGTTGCGAAAAGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATATACACgag                                                                   >  1:4773619/1‑68 (MQ=255)
     gCAAAGTTGCGAAAAGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGta                                                                 >  1:5827092/1‑71 (MQ=255)
     gCAAAGTTGCGAAAAGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGta                                                                 >  1:2099612/1‑71 (MQ=255)
      cAAAGTTGCGAAAAGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGtat                                                                <  1:1030291/71‑1 (MQ=255)
      cAAAGTTGCGAAAAGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGtat                                                                <  1:7234/71‑1 (MQ=255)
       aaaGTTGCGAAAAGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGtata                                                               >  1:5277315/1‑71 (MQ=255)
           ttGCGAAAAGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATAtact                                                           <  1:18310/71‑1 (MQ=255)
           ttGCGAAAAGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATAtact                                                           <  1:4440298/71‑1 (MQ=255)
               gAAAAGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTTGCGTATGTACTCgt                                                                    <  1:753389/58‑1 (MQ=255)
               gAAAAGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATAtac                                                            <  1:3917039/66‑1 (MQ=255)
                 aaaGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGtata                                                               >  1:2412695/1‑61 (MQ=255)
                 aaaGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGtat                                                                >  1:3713928/1‑60 (MQ=255)
                 aaaGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACt                                                     >  1:5386210/1‑71 (MQ=255)
                  aaGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCgtgt                                                                  >  1:5797082/1‑57 (MQ=255)
                  aaGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCg                                                                     >  1:6716249/1‑54 (MQ=255)
                  aaGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATAtac                                                            <  1:4702933/63‑1 (MQ=255)
                  aaGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATAtac                                                            <  1:5777673/63‑1 (MQ=255)
                  aaGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATATACACGAGTACAtac                                                            >  1:6630367/1‑63 (MQ=37)
                   aGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTcc                                                   >  1:768251/1‑71 (MQ=255)
                    gCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATATACACGAGtacat                                                              <  1:1425664/59‑1 (MQ=37)
                     cAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCgt                                                                    <  1:7774705/52‑1 (MQ=255)
                       aCGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTaa                                                >  1:6079271/1‑70 (MQ=255)
                        cGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTaaaa                                              <  1:261475/71‑1 (MQ=255)
                        cGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTaaaa                                              <  1:3396519/71‑1 (MQ=255)
                         gTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCgt                                                                    <  1:6269075/48‑1 (MQ=255)
                         gTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTaaaaa                                             <  1:417023/71‑1 (MQ=255)
                           gCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATAtacta                                                          >  1:6812811/1‑56 (MQ=255)
                           gCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCa                                                       >  1:5449811/1‑59 (MQ=255)
                           gCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCa                                                       >  1:7924128/1‑59 (MQ=255)
                           gCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTaaaaaa                                            <  1:5303238/70‑1 (MQ=255)
                            ccTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAAcc                                          >  1:2527607/1‑71 (MQ=255)
                              tGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCAc                                                      <  1:77936/57‑1 (MQ=255)
                              tGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCg                                         <  1:5287973/70‑1 (MQ=255)
                               gcgcTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCgtgt                                                                  >  1:6480723/1‑44 (MQ=255)
                               gcgcTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCgtgt                                                                  >  1:4228408/1‑44 (MQ=255)
                                cgcTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGaa                                       >  1:3240231/1‑70 (MQ=255)
                                cgcTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAAc                                      <  1:7361638/71‑1 (MQ=255)
                                cgcTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAAc                                      >  1:1996168/1‑71 (MQ=255)
                                cgcTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAAc                                      <  1:1667475/71‑1 (MQ=255)
                                 gcTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAAcc                                          >  1:7015197/1‑66 (MQ=255)
                                 gcTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACt                                     >  1:4035675/1‑71 (MQ=255)
                                 gcTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACt                                     >  1:4219807/1‑71 (MQ=255)
                                 gcTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACt                                     <  1:2762054/71‑1 (MQ=255)
                                 gcTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTACTAAAAAACCGAACt                                     >  1:1984956/1‑71 (MQ=255)
                                  cTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACt                                     <  1:1091127/70‑1 (MQ=255)
                                  cTGGAAGCATGCCCGCAAAAACGTGGCGTATATACACgagt                                                                  <  1:1933935/41‑1 (MQ=37)
                                  cTGGAAGCATGCCCGCAAAAACGTGGCGTATATACACgagt                                                                  <  1:361121/41‑1 (MQ=37)
                                   tGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCt                                                  <  1:6500135/56‑1 (MQ=255)
                                   tGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCt                                                  <  1:875206/56‑1 (MQ=255)
                                     gAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGta                                                                 <  1:3814217/39‑1 (MQ=255)
                                     gAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCg                                         >  1:7757343/1‑63 (MQ=255)
                                     gAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAAcacg                                   <  1:1113090/69‑4 (MQ=255)
                                      aaGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTa                                                 <  1:6615270/54‑1 (MQ=255)
                                      aaGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAAc                                           <  1:1494498/60‑1 (MQ=255)
                                       aGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATAtactac                                                         >  1:2623974/1‑45 (MQ=255)
                                       aGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACt                                                     >  1:4764968/1‑49 (MQ=255)
                                       aGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCcgcg                                >  1:5141936/1‑70 (MQ=255)
                                       aGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCgcgc                               >  1:1488801/1‑71 (MQ=255)
                                        gCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCg                                         <  1:251092/60‑1 (MQ=255)
                                           tGCCCGCAAAAACGTGGCGTATGTACTCGTGtata                                                               <  1:7699807/35‑1 (MQ=255)
                                            gCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGc                            >  1:7873005/1‑69 (MQ=255)
                                            gCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCg                           >  1:2809676/1‑70 (MQ=255)
                                             cccGCAGAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTa                         <  1:492416/71‑1 (MQ=255)
                                             cccGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTaaaaaa                                            >  1:5104206/1‑52 (MQ=255)
                                              ccGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTaa                        <  1:2659589/71‑1 (MQ=255)
                                              ccGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTa                         >  1:5472065/1‑70 (MQ=255)
                                                gCAAAAACGTGGCGTATGTACTCGTGTATAtactac                                                         >  1:5388511/1‑36 (MQ=255)
                                                gCAAAAACGTGGCGTATGTACTCGTGTATAtacta                                                          >  1:6076105/1‑35 (MQ=255)
                                                 cAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAg                      >  1:1894253/1‑70 (MQ=255)
                                                 cAAAAACGTGGCGTATGTACTAGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGt                     <  1:4184770/71‑1 (MQ=255)
                                                  aaaaaCGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCgcgc                               <  1:4277843/60‑1 (MQ=255)
                                                  aaaaaCGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCgcgc                               <  1:3486668/60‑1 (MQ=255)
                                                  aaaaaCGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGTa                    >  1:3306386/1‑71 (MQ=255)
                                                  aaaaaCGTGGCGTATGTACTCGTGTATATAATACCACTCCTAAAAAACCGAACTc                                    >  1:6245973/1‑55 (MQ=255)
                                                   aaaaCGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGTAt                   <  1:5843092/71‑1 (MQ=255)
                                                   aaaaCGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGTAt                   <  1:7779274/71‑1 (MQ=255)
                                                    aaaCGTGGCGTATGTACTCGTGTATATAGTACCACTCCTaaaaa                                             <  1:7130221/44‑1 (MQ=255)
                                                    aaaCGTGGCGTATGTACTCGTGTATATACTACCACTCCTaaaa                                              <  1:4988596/43‑1 (MQ=255)
                                                      aCGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGTATGcc                >  1:3117270/1‑71 (MQ=255)
                                                      aCGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGTATGcc                >  1:202232/1‑71 (MQ=255)
                                                       cGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCt                              <  1:89830/56‑1 (MQ=255)
                                                       cGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCt                              <  1:2227538/56‑1 (MQ=255)
                                                        gTGGCGTATGTACTCGTGTATATACTACCACTCCTaaaa                                              <  1:4721659/39‑1 (MQ=255)
                                                           tagTATATACACGAGTACATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGTa                    <  1:747112/60‑1 (MQ=25)
                                                            cGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGc                            >  1:4386817/1‑53 (MQ=255)
                                                            cGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGTATGCCGTGTTc          <  1:1657448/71‑1 (MQ=255)
                                                               aTGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGTATGCCgtgt            >  1:1987114/1‑66 (MQ=255)
                                                               aTGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGTATGCCGTGTTCGTc       >  1:1553047/1‑71 (MQ=255)
                                                                tGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGTATGcc                >  1:1162187/1‑61 (MQ=255)
                                                                tGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGTATGCCGTGTTCGTCt      <  1:2060190/71‑1 (MQ=255)
                                                                   aCTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGTATGc                 >  1:6735771/1‑57 (MQ=255)
                                                                    cTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTaa                        >  1:3807858/1‑49 (MQ=255)
                                                                    cTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGTATGCCGTGTTCGTCTGACt  <  1:1276341/71‑1 (MQ=255)
                                                                     tCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGTATGCCGTGTTCGTCTGACt  >  1:7041087/1‑70 (MQ=255)
                                                                     tCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGTATGCCGTGTTCGTCTGACt  >  1:6338513/1‑70 (MQ=255)
                                                                     |                                                                     
TGCTCGCAAAGTTGCGAAAAGCAACGTGCCTGCGCTGGAAGCATGCCCGCAAAAACGTGGCGTATGTACTCGTGTATATACTACCACTCCTAAAAAACCGAACTCCGCGCTGCGTAAAGTATGCCGTGTTCGTCTGACT  >  AP009048/4165899‑4166037

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: