Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 1,992,583 Δ1 bp 9.1% coding (942/1317 nt) shiA → shikimate transporter

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6061,992,5830T→. 9.1% 9.6 ‑0.5 ‑0.544coding (942/1317 nt)shiAshikimate transporter
Reads supporting (aligned to +/- strand):  new base (2/2):  ref base (13/27):  total (15/29)
Fisher's exact test strand distribution p-value = 5.96e-01
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 3.12e-01

TTCCCTGTTTTGCCTGGCTTGCCGATCGTTTTGGTCGCCGTAGGGTTTATATCACAGGTACGTTAATCGG  >  REL606/1992549‑1992618
                                  |                                   
ttCCCTGTTTTGCCTGGCTTGCGGATCGTTTTGGTc                                    <  1:6422505/36‑1 (MQ=255)
ttCCCTGTTTTGCCTGGCTTGCCGATCGTTTTGGTc                                    <  1:6234357/36‑1 (MQ=255)
 tCCCTGTTTTGCCTGGCTTGCCGATCGTTTTGGTCg                                   >  1:6670589/1‑36 (MQ=255)
 tCCCTGTTTTGCCTGGCTTGCCGATCGTTTTGGTCg                                   <  1:4548347/36‑1 (MQ=255)
 tCCCTGTTTTGCCTGATTTGCCGATCGTTTTGGTCg                                   <  1:4463400/36‑1 (MQ=37)
   ccTGTTTTGCCTGGCTTGCCGATCGTTTTGGTCGcc                                 <  1:1864343/36‑1 (MQ=255)
    cTGTTTTGCCTGGCTTGCCGATCGTTTTGGTCGCCg                                >  1:1954503/1‑36 (MQ=255)
     tGTTTTGCCTGGCTTGCCGATCGTTTTTGTCGCCGt                               >  1:5111712/1‑36 (MQ=255)
     tGTTTTGCCTGGCTTGCCGATCGTTTTGGTCGCCGt                               <  1:6792524/36‑1 (MQ=255)
      attttGCCTGGCTTGCCGATCGTTTTGGTCGCCGTa                              <  1:359803/35‑1 (MQ=255)
       ttttGCCTGGCTTGCCGATCGTTTTGGTCGCCGTAg                             <  1:1179185/36‑1 (MQ=255)
        tttGCCTGGCTTGCCGATCGTTTTTGTCGCCGtttg                            >  1:3225395/1‑33 (MQ=37)
         ttGCCTGGCTTGCCGATCGTTTTGGTCGCCGTAggg                           <  1:4642906/36‑1 (MQ=255)
           gCCTGGCTTGCCGATCGTTTTGG.CGCCGTAGGGttt                        >  1:168585/1‑36 (MQ=38)
            ccTGGCTTGCCGATCGTTTTGGTCGCCGTAGGGttt                        <  1:7252315/36‑1 (MQ=255)
            ccTGGCTTGCCGATCGTTTTGGTCGCCGTAGGGttt                        >  1:5875596/1‑36 (MQ=255)
             cTGGCTTGCCGATCGTTTTGGTCGCCGTAGGGTTta                       <  1:7685091/36‑1 (MQ=255)
             cTGGCTTGCCGATCGTTTTGGTCGCCGTAGGGTTta                       <  1:2420249/36‑1 (MQ=255)
              tGGCTTGCCGATCGTTTTGGTGGCCATAGGGTTtat                      >  1:1485481/1‑36 (MQ=37)
              tGGCTTGCCGATCGTTTTGGTCGCCGTAGGGTTtat                      >  1:1335032/1‑36 (MQ=255)
              tGGCTTGCCGATCGTTTTGGTCGCCGTAGGGTTtat                      <  1:6464412/36‑1 (MQ=255)
               ggCTTGCCGATCGTTTTGG.CGCCGTAGGGTTTatat                    <  1:7714953/36‑1 (MQ=38)
                   tGCCGATCGTTTTGGTCGCCGTAGGGTTTATATcac                 <  1:3595082/36‑1 (MQ=255)
                    gCCGATCGTTTTGGTCGCCGTAGGGTTTATATcaca                <  1:3946616/36‑1 (MQ=255)
                      cGATCGTTTTGGTCGCCGTAGGGTTTATATCACAgg              >  1:6035482/1‑36 (MQ=255)
                      cGATCGTTTTGG.CGCCGTAGGGTTTATATCACAGGt             <  1:901656/36‑1 (MQ=38)
                      cGATCGTTTTGG.CGCCGTAGGGTTTATATCACAGGt             >  1:7076978/1‑36 (MQ=38)
                       gATCGTTTTGGTCGCCGTAGTGTTTATATCCCAGGt             <  1:6072382/36‑1 (MQ=37)
                       gATCGTTTTGGTCGCCGTAGGGTTTATATCACAGGt             >  1:3567964/1‑36 (MQ=255)
                       gATCGTTTTGGTCGCCGTAGGGTTTATATCACAGGt             <  1:6554632/36‑1 (MQ=255)
                         tCGTTTTGGTCGCCGTAGGGTTTATATCACAGGTAc           <  1:4899522/36‑1 (MQ=255)
                          cGTTTTGGTCGCCGTAGGGTTTATATCACAGGTACg          >  1:5044180/1‑36 (MQ=255)
                          cGTTTTGGTCGCCGTAGGGTTTATATCACAGGTACg          <  1:61051/36‑1 (MQ=255)
                           gtcttGGTCGCCGTAGGGTTTATATCACAGGTACGt         >  1:1769333/4‑36 (MQ=255)
                            ttttGGTCGCCGTAGGGTTTATATCACAGGTACGtt        <  1:5977800/36‑1 (MQ=255)
                             tttGGTCGCCGTCGGGTTTATATCACAGGTACGTTa       <  1:7527138/36‑1 (MQ=255)
                             tttGGTCGCCGTAGGGTTTATATCACAGGTACGTTa       >  1:1715475/1‑36 (MQ=255)
                             tttGGTCGCCGTAGGGTTTATATCACAGGTACGTTa       <  1:1337664/36‑1 (MQ=255)
                             tttGGTCGCCGTAGGGTTTATATCACAGGTACGTTa       <  1:640935/36‑1 (MQ=255)
                              ttGGTCGCCGTAGGGTTTATATCACAGGTACGTTaa      <  1:5443879/36‑1 (MQ=255)
                               tGGTCGCCGTAGGGTTTATATCACAGGTACGTTAAt     <  1:3590827/36‑1 (MQ=255)
                               tGGTCGCCGTAGGGTTTATATCACAGGTACGTTAAt     <  1:5156967/36‑1 (MQ=255)
                                ggTCGCCGTAGGGTTTATATCACAGGTACGTTAATc    <  1:3359351/36‑1 (MQ=255)
                                 gTCGCCGTAGGGTTTATATCACAGGTACGTTAATCg   >  1:6637510/1‑36 (MQ=255)
                                  tCGCCGTAGGGTTTATATCACAGGTACGTTAATCgg  <  1:4546426/36‑1 (MQ=255)
                                  tCGCCGTAGGGTTTATATCACAGGTACGTTAATCgg  <  1:6369923/36‑1 (MQ=255)
                                  |                                   
TTCCCTGTTTTGCCTGGCTTGCCGATCGTTTTGGTCGCCGTAGGGTTTATATCACAGGTACGTTAATCGG  >  REL606/1992549‑1992618

Base quality scores:  ATCG  < 3 ≤  ATCG  < 13 ≤  ATCG  < 22 ≤  ATCG  < 30 ≤  ATCG  < 37 ≤  ATCG