Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AP009048	3,249,944	C→A	9.9%	P89T (CCG→ACG)	yqjG →	predicted S‑transferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AP009048	3,249,944	0	C	A	9.9%	223.7 / 6.7	70	P89T (CCG→ACG)	yqjG	predicted S‑transferase
Reads supporting (aligned to +/- strand):  ref base C (30/33);  new base A (3/4);  total (33/37)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.28e-01

CGCACCGCACGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCAACCGGAGACACGCTCTA  >  AP009048/3249876‑3250011                                                                     |                                                                    cgcaccgcacGCTGATCATGCGCAAACTCAAAGGACTGGAACCTTTTATTTCCGTTTCCGTAGTGAAccc                                                                    <  1:5148837/70‑1 (MQ=255)  gcaccgcacGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGc                                                                  <  1:4766987/71‑1 (MQ=255)   caccgcacGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCt                                                                 >  1:730997/1‑71 (MQ=255)   caccgcacGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCt                                                                 <  1:3632376/71‑1 (MQ=255)     ccgcacGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGc                                                                  >  1:5114746/1‑68 (MQ=255)     ccgcacGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCt                                                                 <  1:728357/69‑1 (MQ=255)       gcacTCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATg                                                             <  1:2214512/71‑1 (MQ=255)       gcacGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATg                                                             >  1:2230789/1‑71 (MQ=255)        cacGCTGATCATGCTCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGc                                                            <  1:2194682/71‑1 (MQ=255)        cacGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGc                                                            >  1:645208/1‑71 (MQ=255)        cacGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGc                                                            >  1:3531655/1‑71 (MQ=255)                  aTGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACgg                                                  <  1:1577801/71‑1 (MQ=255)                  aTGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACgg                                                  <  1:1553367/71‑1 (MQ=255)                  aTGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACgg                                                  <  1:2733541/71‑1 (MQ=255)                  aTGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACg                                                   <  1:1505165/70‑1 (MQ=255)                     cgcAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTg                                               <  1:2645548/71‑1 (MQ=255)                     cgcAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTg                                               <  1:1132116/71‑1 (MQ=255)                       cAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACACGCTGATGCTGGaaaa                                                     >  1:4825644/1‑63 (MQ=255)                          aCTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAAccc                                                                    <  1:3256975/45‑1 (MQ=255)                          aCTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTg                                               >  1:3305938/1‑66 (MQ=255)                             cAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGa                                             >  1:1138120/1‑65 (MQ=255)                             cAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCttt                                        >  1:4998757/1‑70 (MQ=255)                             cAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACACGCTGATGCTGGAAAACGGTTGGAcc                                           <  1:1290338/67‑1 (MQ=255)                              aaaGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCttt                                        <  1:3676076/69‑1 (MQ=255)                              aaaGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTtga                                      >  1:19343/1‑71 (MQ=255)                              aaaGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTtg                                       <  1:1450103/70‑1 (MQ=255)                               aaGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTtgat                                     <  1:2026842/71‑1 (MQ=255)                               aaGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTtgat                                     >  1:2527548/1‑71 (MQ=255)                                aGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATg                                                             >  1:2512200/1‑46 (MQ=255)                                aGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACgg                                                  <  1:3060217/57‑1 (MQ=255)                                  gACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGaa                                                       <  1:634139/50‑1 (MQ=255)                                  gACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTtgatga                                   >  1:2946178/1‑70 (MQ=255)                                   aCTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTTGAAAACGGTTGGACCTTTGATGACa                                 <  1:3501452/71‑1 (MQ=255)                                    cTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAg                                >  1:3124445/1‑71 (MQ=255)                                       gAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGttt                             >  1:5073628/1‑71 (MQ=255)                                       gAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGttt                             <  1:1744831/71‑1 (MQ=255)                                         aCCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTc                           >  1:790501/1‑71 (MQ=255)                                          ccGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCttt                                        <  1:3468327/57‑1 (MQ=255)                                          ccGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTcc                          <  1:3288837/71‑1 (MQ=255)                                            gTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCgg                        <  1:1094442/71‑1 (MQ=255)                                            gTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCgg                        <  1:2998027/71‑1 (MQ=255)                                            gTTTATTTCCGTTTCCGTAGTGAACACGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCgg                        <  1:3897780/71‑1 (MQ=255)                                            gTTTATTTCCGTTTCAGTAGTGAACACGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCgg                        <  1:4760233/71‑1 (MQ=255)                                             tttATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCggg                       <  1:1570003/71‑1 (MQ=255)                                              ttATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCgg                        >  1:5296767/1‑69 (MQ=255)                                               tATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGaaaa                                                     >  1:3723995/1‑39 (MQ=255)                                               tATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGa                      <  1:4035196/70‑1 (MQ=255)                                               tATTTCCGTTTCCGTAGTGAACACGCTGATGCTGGaaaa                                                     >  1:2032085/1‑39 (MQ=255)                                                 tttccgtttccgTAGTGAACCCGCTGATGCTGGAAAAc                                                    >  1:4056306/1‑38 (MQ=255)                                                   tgcgtttccgtAGTGAACACGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGa                      >  1:1407495/3‑66 (MQ=255)                                                     cgtttccgtAGTGAACCGGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCAAcc                <  1:4261569/70‑1 (MQ=255)                                                     cgtttccgtAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCAACCg               <  1:1677239/71‑1 (MQ=255)                                                        ttccgtAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCg                         >  1:1846811/1‑58 (MQ=255)                                                         tccgtAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCgg                        >  1:2382326/1‑58 (MQ=255)                                                          ccgtAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAg                     >  1:1251087/1‑60 (MQ=255)                                                           cgtAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCAACCGGAGac          <  1:3662168/70‑1 (MQ=255)                                                              aGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCg                         >  1:1695041/1‑52 (MQ=255)                                                              aGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCg                         <  1:5007773/52‑1 (MQ=255)                                                              aGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCAACCGGAGACACGc      >  1:3270550/1‑71 (MQ=255)                                                              aGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCAACCGGAGACACGc      >  1:187630/1‑71 (MQ=255)                                                               gTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCAACCGGAGACACGct     >  1:4136144/1‑71 (MQ=255)                                                                tGAACCCGCTGATGCTGGAAAACGGTTGGACCttt                                        <  1:3755496/35‑1 (MQ=255)                                                                tGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAg                                <  1:3939133/43‑1 (MQ=255)                                                                tGAACCCGATGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCaa                  <  1:613215/57‑1 (MQ=255)                                                                 gAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCgg                        >  1:35241/1‑50 (MQ=255)                                                                 gAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCgg                        >  1:3516083/1‑50 (MQ=255)                                                                  aaCCCGCTGATGCTGGAAAACGGTTGGACCTTtga                                      >  1:186008/1‑35 (MQ=255)                                                                  aaCCCGCTGATGCTGGAAAACGGTTGGACCTTtga                                      >  1:931889/1‑35 (MQ=255)                                                                  aaCCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCAAcc                <  1:40959/57‑1 (MQ=255)                                                                  aaCCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCAACCGGAGACACGCTCTa  >  1:4425536/1‑71 (MQ=255)                                                                  aaCCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCAACCGGAGACACGCTCTa  <  1:939807/71‑1 (MQ=255)                                                                  aaCACGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCAACCGGAGACACGCTCTa  <  1:5181491/71‑1 (MQ=255)                                                                     |                                                                    CGCACCGCACGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCAACCGGAGACACGCTCTA  >  AP009048/3249876‑3250011

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: ‑