Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	3,846,918	T→C	36.8%	V62A (GTT→GCT)	htrL →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,846,918	0	T	C	36.8%	42.2 / 61.0	57	V62A (GTT→GCT)	htrL	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (12/24);  new base C (8/13);  total (20/37)
Fisher's exact test for biased strand distribution p-value = 7.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.37e-01

CTTTGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGATAT  >  W3110S.gb/3846850‑3846985                                                                     |                                                                    cTTTGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTg                                                                   <  1:4281341/71‑1 (MQ=255)    tGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGaa                                                                 >  1:4004173/1‑70 (MQ=255)    tGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAg                                                                >  1:4303805/1‑71 (MQ=255)            tGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCg                                                         >  1:436037/1‑70 (MQ=255)             ggCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGc                                                        >  1:296530/1‑70 (MQ=255)             ggCCGCACTTGAAAATGAGATCATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGc                                                        >  1:2665766/1‑70 (MQ=255)              gCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCa                                                       <  1:4305073/70‑1 (MQ=255)              gCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGc                                                        <  1:1129114/69‑1 (MQ=255)              gCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGc                                                        <  1:2469616/69‑1 (MQ=255)               ccGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGc                                                        <  1:1352281/68‑1 (MQ=255)                   aCTTGAAAATGAGATGATTATTTTCACTTCTCCCTATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGaa                                                 <  1:4758159/71‑1 (MQ=255)                   aCTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGaa                                                 <  1:984773/71‑1 (MQ=255)                   aCTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGaa                                                 <  1:3176042/71‑1 (MQ=255)                   aCTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGaa                                                 <  1:4042053/71‑1 (MQ=255)                   aCTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGaa                                                 <  1:2990912/71‑1 (MQ=255)                    cTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAg                                                                >  1:2943715/1‑55 (MQ=255)                    cTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGaa                                                 >  1:1622311/1‑70 (MQ=255)                     ttGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGaa                                                 <  1:1510072/69‑1 (MQ=255)                      tGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAAc                                              >  1:4304784/1‑71 (MQ=255)                        aaaaTGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAAcc                                             <  1:2690876/70‑1 (MQ=255)                        aaaaTGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAAcc                                             <  1:2698598/70‑1 (MQ=255)                         aaaTGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACcaa                                           <  1:2980956/71‑1 (MQ=255)                                    ttattTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGGGATTCGCAACGGAAAACCAACAACGgttatc                                >  1:1225444/1‑71 (MQ=255)                                     tattTTCACTTCTCCCGATTTGAAACCAAGGGTTg                                                                   >  1:3718567/1‑35 (MQ=255)                                     tattTTCACTTCTCCCGATTTGAAACCAAGGGTTg                                                                   >  1:2982369/1‑35 (MQ=255)                                     tattTTCACTTCTCCCGATTTGAAACCAAGGGTTg                                                                   >  1:4009458/1‑35 (MQ=255)                                     tattTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACcaac                                          <  1:604408/60‑1 (MQ=255)                                     tattTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACcaac                                          <  1:925310/60‑1 (MQ=255)                                      attTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgt                              >  1:3384484/1‑71 (MQ=255)                                      attTTCACTTCTCACGATTTGAAACCAAGGGTTGAAGCGAtt                                                           >  1:779413/1‑42 (MQ=255)                                       ttttCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgtt                             <  1:688860/71‑1 (MQ=255)                                       ttttCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACcaac                                          <  1:2453596/58‑1 (MQ=255)                                         ttCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgttat                           >  1:3034943/1‑71 (MQ=255)                                          tCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgttatc                          >  1:4173437/1‑71 (MQ=255)                                          tCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgttat                           >  1:644194/1‑70 (MQ=255)                                          tCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgttat                           >  1:147559/1‑70 (MQ=255)                                             cTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACcaac                                          <  1:4918136/52‑1 (MQ=255)                                              ttCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGc                                                        <  1:132197/37‑1 (MQ=255)                                              ttCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGgttatc                                <  1:4906490/61‑1 (MQ=255)                                                 tcCCGATTTGAAACCAATGGTTGAAGCGATTCGCAACGGAAAACcaacaa                                        <  1:1277130/50‑1 (MQ=255)                                                 tcCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACcaacaa                                        <  1:907040/50‑1 (MQ=255)                                                  cccGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGgtt                                   >  1:2405760/1‑54 (MQ=255)                                                   ccGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATaaaa                 <  1:2318224/71‑1 (MQ=255)                                                   ccGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATaa                   <  1:3186439/69‑1 (MQ=255)                                                   ccGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATaa                   <  1:2314153/69‑1 (MQ=255)                                                    cGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACcaac                                          <  1:3840364/45‑1 (MQ=255)                                                      aTTTGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACca                                            <  1:4811373/41‑1 (MQ=255)                                                        ttGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACcaac                                          >  1:4728040/1‑41 (MQ=255)                                                         tGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGaa            <  1:4580484/70‑1 (MQ=255)                                                         tGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGaa            <  1:4503244/70‑1 (MQ=255)                                                         tGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGaa            <  1:4919402/70‑1 (MQ=255)                                                           aaaCCAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATaaa                  <  1:1836296/62‑1 (MQ=255)                                                           aaaCCAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATaaa                  <  1:4475408/62‑1 (MQ=255)                                                               cAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGa     <  1:3495054/71‑1 (MQ=255)                                                               cAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGa     <  1:3143469/71‑1 (MQ=255)                                                                  gggTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGatat  <  1:446916/71‑1 (MQ=255)                                                                  gggTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGatat  <  1:978484/71‑1 (MQ=255)                                                                     |                                                                    CTTTGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGATAT  >  W3110S.gb/3846850‑3846985

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑