Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,217,476	T→C	6.4%	I37I (ATT→ATC)	ycgZ →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,217,476	0	T	C	6.4%	171.3 / 3.9	62	I37I (ATT→ATC)	ycgZ	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (25/33);  new base C (2/2);  total (27/35)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.46e-01

ACTCGTTACTTTGCAAAAGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTTGTGCCAAACTTCTTTGCCGACTGGAAC  >  W3110S.gb/1217408‑1217540                                                                     |                                                                 aCTCGTTACTTTGCAAAAGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGAtttt                                                                >  1:234222/1‑71 (MQ=255) aCTCGTTACTTTGCAAAAGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGAtttt                                                                >  1:348325/1‑71 (MQ=255)     gTTACTTTGCAAAAGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGaaa                                                            <  1:1210546/71‑1 (MQ=255)     gTTACTTTGCAAAAGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGaaa                                                            <  1:3938539/71‑1 (MQ=255)     gTTACTTTGCAAAAGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGaaa                                                            <  1:2491757/71‑1 (MQ=255)     gTTACTTCGCAAAAGCTAACTTGCATTCTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGaaa                                                            <  1:740724/71‑1 (MQ=255)        aCTTTGCAAAAGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGAt                                                         >  1:3006325/1‑71 (MQ=255)        aCTTTGCAAAAGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGAt                                                         >  1:3593840/1‑71 (MQ=255)        aCTTTGCAAAAGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGAt                                                         >  1:2123322/1‑71 (MQ=255)        aCTTTGCAAAAGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGAt                                                         >  1:2393036/1‑71 (MQ=255)        aCTTTGCAAAAGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGAt                                                         >  1:2047564/1‑71 (MQ=255)         cTTTGCAAAAGGTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATg                                                        <  1:2239536/71‑1 (MQ=255)            tGCAAAAGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATgg                                                       <  1:1646000/69‑1 (MQ=255)            tGCAAAAGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGAc                                                     >  1:1674812/1‑71 (MQ=255)            tGCAAAAGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGAc                                                     >  1:3614940/1‑71 (MQ=255)               aaaaGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTa                                                  <  1:465106/71‑1 (MQ=255)                aaaGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGaa                                                             <  1:4564505/59‑1 (MQ=255)                aaaGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGaa                                                             <  1:3631480/59‑1 (MQ=255)                aaaGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGaa                                                             <  1:478352/59‑1 (MQ=255)                aaaGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTaa                                                 >  1:4489903/1‑71 (MQ=255)                aaaGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTaa                                                 <  1:4478147/71‑1 (MQ=255)                   gCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCt                                              >  1:4057980/1‑71 (MQ=255)                       aCTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATCTTGAAAGATGGACGTCATCTGa                                            <  1:656418/69‑1 (MQ=255)                       aCTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATCTTGAAAGATGGACGTAATCTGa                                            <  1:4738208/69‑1 (MQ=255)                           gCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGa                                       <  1:2041197/70‑1 (MQ=255)                            cATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGa                                       <  1:136314/69‑1 (MQ=255)                               aCTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATCTTGAAAGATGGACGTAATCTGAGTCGAAAGTc                                  >  1:3402480/1‑71 (MQ=255)                                cTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGaaa                                                            >  1:3121637/1‑44 (MQ=255)                                cTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGaaa                                                            >  1:3207321/1‑44 (MQ=255)                                cTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGa                                                          >  1:2207680/1‑46 (MQ=255)                                cTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCg                                 >  1:2049918/1‑71 (MQ=255)                                   agcagGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCtt                              <  1:1602106/71‑1 (MQ=255)                                   agcagGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCtt                              <  1:1079468/71‑1 (MQ=255)                                   agcagGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCt                               <  1:1351794/70‑1 (MQ=255)                                       ggAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCtt                              <  1:514191/67‑1 (MQ=255)                                       ggAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTtgtg                          >  1:3722905/1‑71 (MQ=255)                                       ggAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTtgtg                          >  1:1070495/1‑71 (MQ=255)                                       ggAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTtgtg                          >  1:2211650/1‑71 (MQ=255)                                       ggAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTtgtg                          <  1:1567529/71‑1 (MQ=255)                                       ggAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTtgtg                          <  1:3155904/71‑1 (MQ=255)                                        gAAACTCTCGGGGAAATTGTGACTGAGATTTTGaaa                                                            <  1:516076/36‑1 (MQ=255)                                        gAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTTGTGc                         >  1:2172787/1‑71 (MQ=255)                                          aaCTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTTGTGcc                        >  1:2889406/1‑70 (MQ=255)                                             tctcGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGa                                            <  1:3580167/47‑1 (MQ=255)                                             tctcGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGa                                            <  1:372066/47‑1 (MQ=255)                                              ctcGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTTGTGCCAAAct                   >  1:1510398/1‑71 (MQ=255)                                               tcGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGt                                                   <  1:2775566/38‑1 (MQ=255)                                               tcGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGt                                          >  1:1633075/1‑47 (MQ=255)                                               tcGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTTGTGCCAAAc                    <  1:2974457/69‑1 (MQ=255)                                                 ggggAAATTGTGACTGAGATTTTGAAAGATGGACGTaa                                                 >  1:1572827/1‑38 (MQ=255)                                                    gAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTTGTGCCAAACTTCTTTg             >  1:68814/1‑71 (MQ=255)                                                      aaTTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCg                                        <  1:1777798/42‑1 (MQ=255)                                                       aTTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTtgt                           <  1:713294/54‑1 (MQ=255)                                                       aTTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTTGTGCCAAACTTCTTTGcc           >  1:3967504/1‑70 (MQ=255)                                                         tgtgACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTTGTGCCAAACTTCTTTGCCGAc        >  1:1957228/1‑71 (MQ=255)                                                         tgtgACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTTGTGCCAAACTTCTTTGCCGAc        >  1:466975/1‑71 (MQ=255)                                                          gtgACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTTGTGCCAAACTTCTTTGCCGAc        <  1:1326308/70‑1 (MQ=255)                                                           tgACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTTGTGCCAAACTTCTTTGCCGACTg      <  1:4012452/71‑1 (MQ=255)                                                           tgACTGAGATCTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTtgtg                          >  1:4803442/1‑51 (MQ=255)                                                             aCTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTTGTGCCAAACTTCTTTGCCGACTgg     <  1:25579/70‑1 (MQ=255)                                                              cTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTTGTGCCAAACTTCTTTGCCGACTGGaa   <  1:1037875/71‑1 (MQ=255)                                                               tGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTTGTGCCa                       <  1:1324692/50‑1 (MQ=255)                                                                gagaTTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTTGTGCCAAActtct                <  1:3657525/56‑1 (MQ=255)                                                                 agaTTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTTGTGCCAAACTTCTTTGCCGACTGGAac  <  1:1894534/69‑1 (MQ=255)                                                                     tttGAAAGATGGACGTAATCTGAGTCGAAAGTCGCtt                              <  1:3999818/37‑1 (MQ=255)                                                                     tttGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTTGTGcc                        <  1:810508/43‑1 (MQ=255)                                                                     |                                                                 ACTCGTTACTTTGCAAAAGCTAACTTGCATACTCAGCAGGAAACTCTCGGGGAAATTGTGACTGAGATTTTGAAAGATGGACGTAATCTGAGTCGAAAGTCGCTTTGTGCCAAACTTCTTTGCCGACTGGAAC  >  W3110S.gb/1217408‑1217540

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑