Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AP009048	4,220,646	C→T	15.6%	P527S (CCA→TCA)	aceB →	malate synthase A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AP009048	4,220,646	0	C	T	15.6%	199.9 / 25.2	77	P527S (CCA→TCA)	aceB	malate synthase A
Reads supporting (aligned to +/- strand):  ref base C (38/27);  new base T (10/2);  total (48/29)
Fisher's exact test for biased strand distribution p-value = 1.20e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.93e-01

TTTTGACGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCGTACAC  >  AP009048/4220576‑4220714                                                                       |                                                                     ttttGACGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGc                                                                      <  1:1904572/71‑1 (MQ=255)   ttGACGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGc                                                                      >  1:1944823/1‑69 (MQ=255)   ttGACGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGc                                                                      >  1:320019/1‑69 (MQ=255)    tGACGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAg                                                                   >  1:1705767/1‑71 (MQ=255)       cGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGc                                                                 >  1:1211667/1‑70 (MQ=255)       cGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCt                                                                <  1:3189454/71‑1 (MQ=255)         aTGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGc                                                                      <  1:2728529/63‑1 (MQ=255)             cGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGcc                                                          <  1:4301289/71‑1 (MQ=255)             cGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGcc                                                          <  1:505184/71‑1 (MQ=255)              gCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCt                                                         >  1:3504348/1‑71 (MQ=255)               cACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCt                                                         >  1:1832161/1‑70 (MQ=255)                aCGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGt                                                       >  1:1200837/1‑71 (MQ=255)                aCGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGt                                                       >  1:1353321/1‑71 (MQ=255)                 cGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTACTGACCCTGCCAGGCTACCGCCTGt                                                       >  1:1258804/1‑70 (MQ=255)                  gCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGc                                                                      >  1:1975911/1‑54 (MQ=255)                  gCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGc                                                                 <  1:2313288/59‑1 (MQ=255)                   cTTGATGGAACAGATCACCACTTCCGATTAGTTAATTGATTTCCTGACCCTGCCAGGc                                                                 <  1:4025586/58‑1 (MQ=255)                     tGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCg                                                  >  1:150114/1‑71 (MQ=255)                      gATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGc                                                   >  1:4320286/1‑69 (MQ=255)                      gATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTACTGACCCTGTCAGGCTACCGCCTGTTAGCg                                                  >  1:3526784/1‑70 (MQ=255)                       attgAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGt                                                 >  1:3388613/4‑70 (MQ=255)                       aTGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAg                                                                   >  1:1576999/1‑52 (MQ=255)                       aTGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGt                                                 <  1:1725876/70‑1 (MQ=255)                        tGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCa                                                                    >  1:1043981/1‑50 (MQ=255)                        tGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTaa                                               <  1:2906306/71‑1 (MQ=255)                          gAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAac                                             >  1:4194312/1‑71 (MQ=255)                          gAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAgg                                                                  >  1:3561257/1‑50 (MQ=255)                          gAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAac                                             <  1:3096250/71‑1 (MQ=255)                            aCAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTaaa                                              >  1:2495456/1‑68 (MQ=255)                            aCAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAacca                                           <  1:2149688/71‑1 (MQ=255)                            aCAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAacca                                           <  1:2905029/71‑1 (MQ=255)                             cAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAaccac                                          >  1:3952468/1‑71 (MQ=255)                             cAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAaccac                                          <  1:3141140/71‑1 (MQ=255)                               gATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAaccac                                          <  1:186578/69‑1 (MQ=255)                                aTCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGc                                                   <  1:3936013/59‑1 (MQ=255)                                 tCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTa                                                     >  1:52326/1‑56 (MQ=255)                                  caccacTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTATacca                                           <  1:3381782/65‑1 (MQ=255)                                  caccacTTCCGATGAGTTAATTGATTTCCTGACACTGCCAGGCTACCGCCTGTTAGCGTAAACCACcaca                                      >  1:4459335/1‑70 (MQ=255)                                    ccacTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTa                                                     >  1:1764156/1‑53 (MQ=255)                                       cTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGt                                                       >  1:2894549/1‑48 (MQ=255)                                       cTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTa                                >  1:2907977/1‑71 (MQ=255)                                       cTTCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTa                                >  1:3868413/1‑71 (MQ=255)                                       cTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTa                                >  1:3735173/1‑71 (MQ=255)                                         tCCGATGAGTTAATTGATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATg                              >  1:1362536/1‑71 (MQ=255)                                         tCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATg                              >  1:3825789/1‑71 (MQ=255)                                         tCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATg                              >  1:1814876/1‑71 (MQ=255)                                          ccGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTaaa                                              >  1:4470286/1‑54 (MQ=255)                                          ccGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATg                              >  1:249874/1‑70 (MQ=255)                                           cGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGt                                                       <  1:1271756/44‑1 (MQ=255)                                             aTGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTaaa                                              >  1:4448344/1‑51 (MQ=255)                                             aTGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACcaccac                                       <  1:2979164/58‑1 (MQ=255)                                             aTGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAg                           >  1:4494293/1‑70 (MQ=255)                                             aTGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGc                          <  1:2559733/71‑1 (MQ=255)                                             aTGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGc                          <  1:2832510/71‑1 (MQ=255)                                              tGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAaccacc                                         >  1:3189091/1‑55 (MQ=255)                                                aGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATc                       <  1:458711/71‑1 (MQ=255)                                                    aaTTGATTTCCTGACCCTGCCAGGCTACCGCCTGtt                                                      >  1:2383275/1‑36 (MQ=255)                                                    aaTTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAaccacc                                         <  1:705565/49‑1 (MQ=255)                                                    aaTTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCt                      >  1:1055971/1‑68 (MQ=255)                                                    aaTTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGca                   >  1:2043951/1‑71 (MQ=255)                                                    aaTTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGca                   >  1:813210/1‑71 (MQ=255)                                                     aTTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGc                          <  1:3972692/63‑1 (MQ=255)                                                     aTTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGcac                  <  1:3126994/71‑1 (MQ=255)                                                     aTTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGcac                  <  1:8086/71‑1 (MQ=255)                                                      ttGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGcaca                 <  1:3995554/71‑1 (MQ=255)                                                      ttGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGcaca                 <  1:726640/71‑1 (MQ=255)                                                        gATTTCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACAt                <  1:4382331/70‑1 (MQ=255)                                                          tttCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGaa             <  1:771533/71‑1 (MQ=255)                                                           ttCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGaa             >  1:4560080/1‑70 (MQ=255)                                                            tCCTGACCCTGTCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGaaaa           >  1:3004650/1‑71 (MQ=255)                                                            tCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGaaa            <  1:4514281/70‑1 (MQ=255)                                                              cTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACAt                                     >  1:1331077/1‑43 (MQ=255)                                                               tGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAg                           >  1:227136/1‑52 (MQ=255)                                                               tGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAAccc        >  1:4387624/1‑71 (MQ=255)                                                               tGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAAccc        >  1:1419274/1‑71 (MQ=255)                                                                gACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACAt                                     <  1:1561703/41‑1 (MQ=255)                                                                gACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAAccc        >  1:3442563/1‑70 (MQ=255)                                                                gACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCg       >  1:1012138/1‑71 (MQ=255)                                                                gACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCg       >  1:1838985/1‑71 (MQ=255)                                                                gACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCg       >  1:851421/1‑71 (MQ=255)                                                                      gCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCGTacac  >  1:2224912/1‑70 (MQ=255)                                                                      gCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCGTacac  >  1:2003864/1‑70 (MQ=255)                                                                       ccAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCGTacac  <  1:3842384/69‑1 (MQ=255)                                                                       |                                                                     TTTTGACGATGCCGCACGCTTGATGGAACAGATCACCACTTCCGATGAGTTAATTGATTTCCTGACCCTGCCAGGCTACCGCCTGTTAGCGTAAACCACCACATAACTATGGAGCATCTGCACATGAAAACCCGTACAC  >  AP009048/4220576‑4220714

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: ‑