Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,661,831	A→T	10.9%	R683S (AGA→AGT)	ynfE →	oxidoreductase subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,661,831	0	A	T	10.9%	134.8 / 9.8	55	R683S (AGA→AGT)	ynfE	oxidoreductase subunit
Reads supporting (aligned to +/- strand):  ref base A (33/16);  new base T (2/4);  total (35/20)
Fisher's exact test for biased strand distribution p-value = 1.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.41e-01

TGAAGTGATAAGCCCATTGCCAGTTTATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTACTCACTCGACCTACGGCAATATTGATC  >  W3110S.gb/1661765‑1661901                                                                   |                                                                       tGAAGTGATAAGCCCATTGCCAGTTTATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAAcc                                                                     <  1:1137686/70‑1 (MQ=255)  gAAGTGATAAGCCCATTGCCAGTTTATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCt                                                                    <  1:2279663/70‑1 (MQ=255)       gATAAGCCCATTGCCAGTTTATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCa                                                               >  1:1231985/1‑70 (MQ=255)        aTAAGCCCATTGCCAGTTTATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCAc                                                              >  1:2128832/1‑70 (MQ=255)          aaGCCCATTGCCAGTTTATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCa                                                               >  1:1458573/1‑67 (MQ=255)              ccATTGCCAGTTTATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGc                                                           <  1:2070521/67‑1 (MQ=255)                  tGCCAGTTTATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGtt                                                    >  1:1837125/1‑70 (MQ=255)                   gCCAGTTTATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTcc                                                                 <  1:1476435/56‑1 (MQ=255)                   gCCAGTTTATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTg                                                  >  1:1152018/1‑71 (MQ=255)                     cAGTTTATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCa                                                               >  1:862423/1‑56 (MQ=255)                      aGTTTATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGtt                                               >  1:1684160/1‑71 (MQ=255)                       gTTTATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGttt                                              <  1:1394823/71‑1 (MQ=255)                        tttATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTc                                             <  1:915438/71‑1 (MQ=255)                         ttATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCa                                                               >  1:3199992/1‑52 (MQ=255)                         ttATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTc                                             >  1:2711219/1‑70 (MQ=255)                         ttATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTc                                             >  1:3845798/1‑70 (MQ=255)                          tATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAAc                                                        >  1:3760278/1‑58 (MQ=255)                          tATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTcc                                            <  1:3383420/70‑1 (MQ=255)                          tATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTcc                                            <  1:3022587/70‑1 (MQ=255)                          tATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCa                                           >  1:320121/1‑71 (MQ=255)                               cTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACa                                      <  1:1286405/71‑1 (MQ=255)                                tCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGa                                                                        <  1:3144067/36‑1 (MQ=255)                                  aaCCTTTGAAGGCTGGAACTCCCCTGAACGTAGAAc                                                                      >  1:649557/1‑36 (MQ=255)                                   aCCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTc                                             >  1:2069103/1‑60 (MQ=255)                                   aCCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACATTCCCACTGCaa                                                         >  1:2486990/1‑48 (MQ=255)                                    ccTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATcc                                 >  1:2180833/1‑71 (MQ=255)                                    ccTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTACATTACAAATcc                                 >  1:380389/1‑71 (MQ=255)                                      tttGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTcc                                            <  1:20393/58‑1 (MQ=255)                                       ttGAAGGCTGGGACTCCCCTGAACGTAGTGCCTTCCCACTGCAACTGTTTGGtt                                               >  1:1228532/1‑54 (MQ=255)                                       ttGAAGGCTGGGACTCCCCTGAACGTAGTGCCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCg                               >  1:2417818/1‑70 (MQ=255)                                       ttGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATc                                  >  1:205237/1‑67 (MQ=255)                                       ttGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATc                                  >  1:2982409/1‑67 (MQ=255)                                        tGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTgg                                                 >  1:2511120/1‑51 (MQ=255)                                        tGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTgg                                                 >  1:617338/1‑51 (MQ=255)                                        tGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCg                               <  1:1470801/69‑1 (MQ=255)                                         gAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTa                             <  1:1823279/70‑1 (MQ=255)                                           aGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTact                           >  1:2186926/1‑70 (MQ=255)                                           aGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTT‑GTTTCCATTACAAATCCCGTactca                         >  1:3742672/1‑71 (MQ=255)                                            ggCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTactca                         >  1:869277/1‑71 (MQ=255)                                            ggCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTactca                         >  1:1442192/1‑71 (MQ=255)                                                 gAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACaaa                                    >  1:3307420/1‑55 (MQ=255)                                                  aaCTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTactcactc                      <  1:2291117/68‑1 (MQ=255)                                                      ccccTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTACTCACTCGACCTAc               >  1:1215005/1‑71 (MQ=255)                                                       cccTGAACGTAGTGCCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTACGCACTCGACCTAc               <  1:2799707/70‑1 (MQ=255)                                                       cccTGAACGTAGTGCCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTACGCACTCGACCTAc               <  1:1279315/70‑1 (MQ=255)                                                       cccTGAACGTAGTGCCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTACGCACTCGACCTAc               <  1:3389837/70‑1 (MQ=255)                                                       cccTGAACGTAGTGCCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTACGCACTCGACCTAc               <  1:490354/70‑1 (MQ=255)                                                           gAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTactcac                        >  1:1254483/1‑57 (MQ=255)                                                           gAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTACTCACTCGACCTACGGCaa          >  1:2860299/1‑71 (MQ=255)                                                           gAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTACTCACTCGACCTACGGCaa          >  1:2517836/1‑71 (MQ=255)                                                           gAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTACTCACTCGACCTACGGCaa          >  1:224028/1‑71 (MQ=255)                                                                tAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTACTCACTCGACCTACGGCAATATTg     <  1:3805129/71‑1 (MQ=255)                                                                tAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTACTCACTCGACCTACGGCAATATTg     <  1:3527829/71‑1 (MQ=255)                                                                tAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTACTCACTCGACCTACGGCAATATTg     <  1:190097/71‑1 (MQ=255)                                                                  gAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTACTCACTCGACCTACGGCAATATTGAt   >  1:855367/1‑71 (MQ=255)                                                                  gAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTACTCACTCGACCTACGGCAATATTGAt   >  1:1754073/1‑71 (MQ=255)                                                                   aaCCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTACTCACTCGACCTACGGCAATATTGAtc  <  1:3560632/71‑1 (MQ=255)                                                                   aaCCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTACTCACTCGACCTACGGCAATATTGAtc  <  1:2235744/71‑1 (MQ=255)                                                                   |                                                                       TGAAGTGATAAGCCCATTGCCAGTTTATGCCTCAACCTTTGAAGGCTGGAACTCCCCTGAACGTAGAACCTTCCCACTGCAACTGTTTGGTTTCCATTACAAATCCCGTACTCACTCGACCTACGGCAATATTGATC  >  W3110S.gb/1661765‑1661901

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: ‑