Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AP009048	3,059,788	C→T	12.0%	L95L (CTG→TTG)	yliK →	methylmalonyl‑CoA mutase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AP009048	3,059,788	0	C	T	12.0%	143.3 / 9.3	50	L95L (CTG→TTG)	yliK	methylmalonyl‑CoA mutase
Reads supporting (aligned to +/- strand):  ref base C (24/20);  new base T (2/4);  total (26/24)
Fisher's exact test for biased strand distribution p-value = 4.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.16e-01

ACCGTGGACCATCCGTCAGTATGCTGGTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGCCACCCACCGTGGCTACGACTCC  >  AP009048/3059718‑3059853                                                                       |                                                                  aCCGTGGACCATCCGTCAGTATGCTGGTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAAcc                                                                   <  1:658625/71‑1 (MQ=255)     tGGACCATCCGTCAGTATGCTGGTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGgc                                                               <  1:1031952/71‑1 (MQ=255)        aCCATCCGTCAGTATGCTGGTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACTTGgccgc                                                            <  1:483093/71‑1 (MQ=255)         ccATCCGTCAGTATGCTGGTTTTTCATCAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACTTGgccgcc                                                           <  1:4530961/71‑1 (MQ=255)         ccATCCGTCAGTATGCTGGTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGgccgcc                                                           <  1:4173976/71‑1 (MQ=255)         ccATCCGTCAGTATGCTGGTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGgccgcc                                                           <  1:3837033/71‑1 (MQ=255)          cATCCGTCAGTATGCTGGTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCt                                                                  <  1:3411495/63‑1 (MQ=255)          cATCCGTCAGTATGCTGGTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGTccgccg                                                          <  1:6001/71‑1 (MQ=255)          cATCCGTCAGTATGCTGGTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGGccgccg                                                          >  1:2072593/1‑71 (MQ=255)          cATCCGTCAGTATGCTGGTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGGacgccg                                                          >  1:2591897/1‑71 (MQ=255)              cGTCAGTATGCTGGTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGGCCGCCggg                                                        >  1:2555749/1‑69 (MQ=255)                  aGTATGCTGGTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCCTAACCTGGCCGCCGGGCaaaa                                                   <  1:2123936/70‑1 (MQ=255)                    tATGCTGGTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCCTAACCTGGCCGCCGGGCAAAAAgg                                                <  1:510507/71‑1 (MQ=255)                      tGCTGGTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCTTAACCTGGCCGCCGGGCAAAAAGGTc                                              >  1:1886333/1‑71 (MQ=255)                      tGCTGGTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACTTGGCCGCCGGGCAAAAAGGt                                               >  1:2457804/1‑70 (MQ=255)                      tGCTGGTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGGCCGCCGGGCaaa                                                    <  1:2843388/65‑1 (MQ=255)                       gCTGGTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGGCCGCCGGGCaaa                                                    <  1:4479431/64‑1 (MQ=255)                           gTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTcc                                         <  1:3291023/71‑1 (MQ=255)                           gTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTcc                                         >  1:3850091/1‑71 (MQ=255)                            tttttCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAg                                                 <  1:1866375/62‑1 (MQ=255)                            tttttCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCg                                        >  1:2963606/1‑71 (MQ=255)                             ttttCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGgccgcc                                                           <  1:3992715/51‑1 (MQ=255)                              tttCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGtt                                      >  1:1119798/1‑71 (MQ=255)                              tttCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGt                                       <  1:4306104/70‑1 (MQ=255)                                  aaCAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTg                                                                 >  1:1329373/1‑40 (MQ=255)                                  aaCAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGt                                  <  1:4452924/71‑1 (MQ=255)                                        aaaaGAGTCCAACGCTTTTTATCGCCGTAACTTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGAcc                            <  1:1503837/71‑1 (MQ=255)                                        aaaaGAGTCCAACGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGAc                             >  1:3849642/1‑70 (MQ=255)                                         aaaGAGTCCAACGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCt                           <  1:2826122/71‑1 (MQ=255)                                           agagTCCAACGCTTTTTATCGCCGTAACTTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGAccat                          <  1:3653955/70‑3 (MQ=255)                                                ccAACGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGccacc                    >  1:1573793/1‑71 (MQ=255)                                                 cAACGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGccacc                    >  1:833095/1‑70 (MQ=255)                                                   aCGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGccacccac                 <  1:4379625/71‑1 (MQ=255)                                                   aCGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGccacccac                 >  1:90179/1‑71 (MQ=255)                                                    cGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGCcacccacc                >  1:2695766/1‑71 (MQ=255)                                                    cGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGCcacccacc                >  1:1479848/1‑71 (MQ=255)                                                    cGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGCcacccacc                >  1:697123/1‑71 (MQ=255)                                                    cGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGCcacccacc                >  1:3527856/1‑71 (MQ=255)                                                    cGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGCcacccacc                >  1:405548/1‑71 (MQ=255)                                                     gCTTTTTATCGCCGTAACTTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGAcacccacca               >  1:3555339/1‑70 (MQ=255)                                                     gCTTTTTATCGCCGTAACCTGGCCGCCGGGCaaaaa                                                  >  1:367670/1‑36 (MQ=255)                                                     gCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGCCACCCACCg               <  1:3973057/71‑1 (MQ=255)                                                       tttttATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGCcacccacc                >  1:1720167/1‑68 (MQ=255)                                                       tttttATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGCCACCCACCGTg             >  1:4286621/1‑71 (MQ=255)                                                             tCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGCCACCCACCGTGGCTAc        <  1:3608101/70‑1 (MQ=255)                                                             tCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGCCACCCACCGTGGCTAc        <  1:1830813/70‑1 (MQ=255)                                                               gCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGCCACCCACCGTGGCTACGAc     >  1:2960245/1‑71 (MQ=255)                                                                ccGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGCCACCCACCGTGGCTACGACt    <  1:591621/71‑1 (MQ=255)                                                                  gTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGCCACCCACCGTGGCTACGACTcc  >  1:2610214/1‑71 (MQ=255)                                                                   tAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGa                              >  1:2192192/1‑42 (MQ=255)                                                                   tAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGCCACCCACCGTGGCTACGACTcc  >  1:2870536/1‑70 (MQ=255)                                                                       cTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGttt                                >  1:649751/1‑36 (MQ=255)                                                                       |                                                                  ACCGTGGACCATCCGTCAGTATGCTGGTTTTTCAACAGCAAAAGAGTCCAACGCTTTTTATCGCCGTAACCTGGCCGCCGGGCAAAAAGGTCTTTCCGTTGCGTTTGACCTTGCCACCCACCGTGGCTACGACTCC  >  AP009048/3059718‑3059853

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: ‑