Predicted mutation
evidence seq id position mutation freq annotation gene description
RA AP009048 2,124,804 T→C 9.3% N105D (AAC→GAC)  cpsG ← phosphomannomutase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AP0090482,124,8040TC 9.3% 148.3 / 6.9 55N105D (AAC→GAC) cpsGphosphomannomutase
Reads supporting (aligned to +/- strand):  ref base T (37/12);  new base C (2/3);  total (40/15)
Fisher's exact test for biased strand distribution p-value = 1.24e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

TGGACGTCGCGCAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATGGAACGTGGCG  >  AP009048/2124737‑2124871
                                                                   |                                                                   
tGGACGTCGCGCAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTtat                                                                   >  1:3261104/1‑70 (MQ=255)
tGGACGTCGCGCAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTtat                                                                   >  1:419692/1‑70 (MQ=255)
   aCGTCGCGCAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATc                                                               >  1:4140668/1‑71 (MQ=255)
   aCGTCGCGCAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATc                                                               >  1:4146615/1‑71 (MQ=255)
     gTCGCGCAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTCATAATccg                                                             <  1:2536070/71‑2 (MQ=255)
     gTCGCGCAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTCATAATccg                                                             <  1:14463/71‑2 (MQ=255)
        gcgcAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCg                                                          >  1:785188/1‑71 (MQ=255)
         cgcAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCg                                                          >  1:1724556/1‑70 (MQ=255)
         cgcAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCg                                                          <  1:3453664/70‑1 (MQ=255)
           cAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGAt                                                       >  1:1893587/1‑71 (MQ=255)
            aGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGAt                                                       >  1:4255504/1‑70 (MQ=255)
             gTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTtat                                                                   <  1:4330063/57‑1 (MQ=255)
              tCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTAt                                                    >  1:4888830/1‑71 (MQ=255)
                cGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCg                                                          >  1:165682/1‑63 (MQ=255)
                  gTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTAtggct                                                >  1:1270323/1‑71 (MQ=255)
                       tcCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCgg                                           >  1:4782289/1‑71 (MQ=255)
                       tcCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCgg                                           >  1:677172/1‑71 (MQ=255)
                         cGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAAt                                                                >  1:1216257/1‑48 (MQ=255)
                         cGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAAt                                                                >  1:530795/1‑48 (MQ=255)
                         cGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCgg                                           <  1:4817413/69‑1 (MQ=255)
                         cGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGt                                          >  1:1399690/1‑70 (MQ=255)
                         cGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGt                                          >  1:1558540/1‑70 (MQ=255)
                         cGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGt                                          >  1:2147212/1‑70 (MQ=255)
                         cGCTGATCAGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGt                                          <  1:3351432/70‑1 (MQ=255)
                          gCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTaa                                        <  1:1858093/71‑1 (MQ=255)
                             gATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTa                                                     >  1:5126209/1‑55 (MQ=255)
                                 gggCGAGCCCCCTCGCGAACCAGCTTCATGCCGTAATAATCCAGCGGATTATGGCTGGCGGAAACTTCaa                                  >  1:680952/1‑70 (MQ=255)
                                   gCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATgc                               >  1:3092148/1‑71 (MQ=255)
                                       gCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGAt                                                       >  1:2595128/1‑43 (MQ=255)
                                           ccTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCgtt                                          <  1:941908/52‑3 (MQ=255)
                                           ccTCGCGAACCAGCTTCATGCCGTCATAATCCGATGGATTAt                                                    <  1:1794521/42‑1 (MQ=21)
                                             tCGCGAACCAGCTTCATGCCGTTATAATCCATCGGAt                                                       <  1:501958/37‑1 (MQ=255)
                                             tCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCa                      >  1:558856/1‑70 (MQ=255)
                                             tCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCAc                     >  1:1724150/1‑71 (MQ=255)
                                             tCGCGAACCAGCTTCATGCCGTTATAATCAATCGGATTATGGATGGCg                                            >  1:2878418/1‑48 (MQ=39)
                                             tCGCGAACCAGCTTCATGCCGTCATAATCCGATGGATTAtaa                                                  >  1:1770072/1‑40 (MQ=17)
                                             tCGCGAACCAGCTTCATGCCGTCATAATCCGATGGATTAtaa                                                  >  1:4538865/1‑40 (MQ=17)
                                              cgcgAACCAGCTTCATGCCGTTATAATCCATCGGATTAtgg                                                  >  1:3014188/1‑41 (MQ=255)
                                               gcgAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCaa                                  >  1:2213583/1‑56 (MQ=255)
                                               gcgAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCaa                                  >  1:3533595/1‑56 (MQ=255)
                                               gcgAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGc                   >  1:856133/1‑71 (MQ=255)
                                                 gAACCAGCTTCATGCCGTTATAATCCATCGGATTa                                                     >  1:3681817/1‑35 (MQ=255)
                                                  aaCCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGcc                  >  1:4632099/1‑69 (MQ=255)
                                                   aCCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGcc                  >  1:1178739/1‑68 (MQ=255)
                                                    ccAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGcc                  >  1:744654/1‑67 (MQ=255)
                                                    ccAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCgaga              <  1:5175086/71‑1 (MQ=255)
                                                     cAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACt                                      <  1:3234314/46‑1 (MQ=255)
                                                      aGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATg            >  1:3448658/1‑71 (MQ=255)
                                                       gCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCaa                                  >  1:977954/1‑48 (MQ=255)
                                                       gCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATg                                >  1:2732207/1‑50 (MQ=255)
                                                       gCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATg            >  1:4221058/1‑70 (MQ=255)
                                                       gCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATg            >  1:3532679/1‑70 (MQ=255)
                                                       gCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATg            >  1:3028309/1‑70 (MQ=255)
                                                           cATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATGGaa         <  1:661371/69‑1 (MQ=255)
                                                            aTGCCGTTATAATCCATCTGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATGGAACg       <  1:1810641/70‑1 (MQ=255)
                                                            aTGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATGGAACg       <  1:4373604/70‑1 (MQ=255)
                                                             tGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATGGAACGTg     >  1:2622784/1‑71 (MQ=255)
                                                                cGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATGGAACGTggaa  <  1:1352701/71‑3 (MQ=255)
                                                                  ttATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATGGAACg       <  1:2586809/64‑1 (MQ=255)
                                                                   |                                                                   
TGGACGTCGCGCAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATGGAACGTGGCG  >  AP009048/2124737‑2124871

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: