Predicted mutation
evidence seq id position mutation freq annotation gene description
RA AP009048 3,533,883 T→C 8.2% intergenic (‑24/+125) yiiM ← / ← kdgT conserved hypothetical protein/2‑keto‑3‑deoxy‑D‑gluconate transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AP0090483,533,8830TC 8.2% 168.7 / 6.7 61intergenic (‑24/+125)yiiM/kdgTconserved hypothetical protein/2‑keto‑3‑deoxy‑D‑gluconate transporter
Reads supporting (aligned to +/- strand):  ref base T (29/27);  new base C (2/3);  total (31/30)
Fisher's exact test for biased strand distribution p-value = 6.71e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01

GATAAGCCTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATCCAGGCAGGAACTC  >  AP009048/3533814‑3533951
                                                                     |                                                                    
gATAAGCCTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTc                                                                     <  1:1443319/71‑1 (MQ=255)
  tAAGCCTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAAttt                                                                      <  1:4304661/68‑1 (MQ=255)
  tAAGCCTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTccc                                                                   <  1:3418220/71‑1 (MQ=255)
  tAAGCCTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTccc                                                                   >  1:4519588/1‑71 (MQ=255)
   aaGCCTGAATCTTGCCTGTGTATACATCACCCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTccc                                                                   >  1:1068702/1‑70 (MQ=255)
    aGCCTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAAttt                                                                      >  1:1222365/1‑66 (MQ=255)
    aGCCTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTcccc                                                                  <  1:132765/70‑1 (MQ=255)
    aGCCTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTcccc                                                                  <  1:2978461/70‑1 (MQ=255)
    aGCCTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCa                                                                 >  1:1650069/1‑71 (MQ=255)
     gCCTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCAt                                                                >  1:3676580/1‑71 (MQ=255)
       cTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTa                                                              <  1:712341/71‑1 (MQ=255)
       cTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTa                                                              <  1:3014583/71‑1 (MQ=255)
        tGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAAttt                                                                      >  1:3443771/1‑62 (MQ=255)
         gAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGa                                                            >  1:3332313/1‑71 (MQ=255)
          aaTCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCa                                                                 >  1:1631539/1‑65 (MQ=255)
           aTCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCAt                                                                >  1:2598405/1‑65 (MQ=255)
                gCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCatat                                                      >  1:1084011/1‑70 (MQ=255)
                   tgtgTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCatat                                                      <  1:4024308/67‑1 (MQ=255)
                    gtgtATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTAGACCAtatttat                                                  >  1:2719858/1‑70 (MQ=255)
                     tgtATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCAtatttat                                                  <  1:3533081/69‑1 (MQ=255)
                     tgtATACATCAACCGGATATCCCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATatttattt                                                <  1:2849888/71‑1 (MQ=255)
                        ataCATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGAcc                                                          >  1:4299541/1‑58 (MQ=255)
                        ataCATCAACCCGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGAcc                                                          >  1:2804281/1‑58 (MQ=255)
                          aCATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATg                                            >  1:936554/1‑70 (MQ=255)
                           cATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCAtattt                                                    <  1:3561238/61‑1 (MQ=255)
                           cATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGt                                           >  1:3176170/1‑70 (MQ=255)
                            aTCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATAtttatttt                                               >  1:2075249/1‑65 (MQ=255)
                             tCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAg                                        <  1:3393894/71‑1 (MQ=255)
                             tCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAg                                        <  1:3125892/71‑1 (MQ=255)
                               aaCCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGc                                      >  1:3304724/1‑71 (MQ=255)
                               aaCCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGc                                      >  1:3218439/1‑71 (MQ=255)
                                aCCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGc                                      >  1:3648854/1‑70 (MQ=255)
                                aCCGGATATCGCATCCGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCg                                     <  1:2739697/71‑1 (MQ=255)
                                  cGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTg                                   <  1:3524653/71‑1 (MQ=255)
                                  cGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTg                                   <  1:3722972/71‑1 (MQ=255)
                                   ggATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATAtttatttta                                              >  1:2610662/1‑59 (MQ=255)
                                        tCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGtt                              <  1:1664259/70‑1 (MQ=255)
                                           cATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCata                                                       <  1:1879923/42‑1 (MQ=255)
                                            aTCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTcgc                         <  1:4501283/71‑1 (MQ=255)
                                               tGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCgg                       >  1:1443209/1‑70 (MQ=255)
                                               tGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCgg                       >  1:1182330/1‑70 (MQ=255)
                                               tGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCgg                       >  1:1500771/1‑70 (MQ=255)
                                                gTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGtt                              <  1:1444489/62‑1 (MQ=255)
                                                 ttCCCTCTCCACGAGAAATTTCCCCATTAGACCAtatt                                                     <  1:373503/38‑1 (MQ=255)
                                                 ttCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTcgcg                        <  1:2390714/67‑1 (MQ=255)
                                                 ttCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGt                      <  1:717461/69‑1 (MQ=255)
                                                  tCCCTCTCCACGTGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAg                   >  1:1967328/1‑71 (MQ=255)
                                                  tCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGt                                           >  1:1632629/1‑47 (MQ=255)
                                                   cccTCTCCACGAGAAATTTCCCCATTAGACCATatttattt                                                >  1:3433892/1‑41 (MQ=255)
                                                   cccTCTCCACGAGAAATTTCCCCATTAGACCATAtttattttat                                             >  1:1883678/1‑44 (MQ=255)
                                                   cccTCTCCACGAGAAATTTCCCCATTAGACCATAtttattttat                                             >  1:2254933/1‑44 (MQ=255)
                                                    ccTCTCCACGAGAAATTTCCCCATTAGACCAtatttatt                                                 <  1:328881/39‑1 (MQ=255)
                                                     ctctCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGt                      <  1:147245/65‑1 (MQ=255)
                                                      tctcCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATc               >  1:1415637/1‑71 (MQ=255)
                                                      tctcCACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAg                   <  1:2539332/67‑1 (MQ=255)
                                                       ctcCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATc               >  1:3966946/1‑70 (MQ=255)
                                                         ccACGAGAAATTTCCCCATTAGACCATAtttatttt                                               <  1:4599654/36‑1 (MQ=255)
                                                           aCGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCg                                     >  1:338590/1‑44 (MQ=255)
                                                            cGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATCcagg           >  1:4496178/1‑69 (MQ=255)
                                                             gagaAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATCcaggca         <  1:2893335/70‑1 (MQ=255)
                                                              agaAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATCcaggcagg       <  1:1585642/71‑1 (MQ=255)
                                                                aaaTTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGttt                             <  1:1540038/47‑1 (MQ=255)
                                                                 aaTTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATCCAGGCAGGAAc    <  1:2750746/71‑1 (MQ=255)
                                                                  aTTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATCCAGGCAGGAACt   >  1:1310594/1‑71 (MQ=255)
                                                                   tttCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATCcagg           <  1:904327/62‑1 (MQ=255)
                                                                   tttCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATCCAGGCAGGAACTc  <  1:4165430/71‑1 (MQ=255)
                                                                   tttCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATCCAGGCAGGAACTc  <  1:1879793/71‑1 (MQ=255)
                                                                    ttCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTc                           >  1:3038262/1‑45 (MQ=255)
                                                                     |                                                                    
GATAAGCCTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATCCAGGCAGGAACTC  >  AP009048/3533814‑3533951

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: