Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	3,764,664	T→C	38.1%	N106D (AAT→GAT)	yidX ←	predicted lipoproteinC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,764,664	0	T	C	38.1%	47.1 / 70.9	63	N106D (AAT→GAT)	yidX	predicted lipoproteinC
Reads supporting (aligned to +/- strand):  ref base T (18/21);  new base C (9/15);  total (27/36)
Fisher's exact test for biased strand distribution p-value = 6.03e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.32e-01

TTTCTTCTTCGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTGAGCATCTT  >  W3110S.gb/3764598‑3764733                                                                   |                                                                      tttCTTCTTCGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATCTaa                                                                    >  1:4912762/1‑70 (MQ=255)  ttcttcttcGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTaa                                                                    <  1:1135931/69‑1 (MQ=255)  ttcttcttcGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTaa                                                                    <  1:3940629/69‑1 (MQ=255)  ttcttcttcGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTaa                                                                    <  1:2604159/69‑1 (MQ=255)          cGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAAt                                                             <  1:4569885/68‑1 (MQ=255)              aTTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCg                                                       <  1:4363146/70‑1 (MQ=255)              aTTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGt                                                      >  1:3847576/1‑71 (MQ=255)              aTTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGt                                                      >  1:129392/1‑71 (MQ=255)              aTTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGt                                                      >  1:568855/1‑71 (MQ=255)                 ccAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCa                                                    <  1:4289164/70‑1 (MQ=255)                  cAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCAt                                                   <  1:3887810/70‑1 (MQ=255)                  cAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCAt                                                   <  1:4032389/70‑1 (MQ=255)                        tagtaAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCtt                                                          <  1:3819910/57‑1 (MQ=255)                        tagtaAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAAt                                                             <  1:2510125/54‑1 (MQ=255)                        tagtaAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAAt                                                             <  1:287712/54‑1 (MQ=255)                          gtaAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAAc                                            >  1:4266555/1‑69 (MQ=255)                          gtaAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCt                                          >  1:4728051/1‑71 (MQ=255)                          gtaAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCt                                          >  1:4045141/1‑71 (MQ=255)                            aaaGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTaa                                                                    <  1:2775939/43‑1 (MQ=255)                            aaaGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCAt                                                   >  1:2747561/1‑60 (MQ=255)                            aaaGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTg                                         >  1:1721491/1‑70 (MQ=255)                             aaGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACGAATCTTGCGTCATCGGCAACCTGaa                                       >  1:4666359/1‑71 (MQ=255)                             aaGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCg                                                       >  1:2934528/1‑55 (MQ=255)                               gCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAata                                     >  1:960707/1‑71 (MQ=255)                                  atatTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATtg                                  <  1:534224/71‑1 (MQ=255)                                   tatTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATtgt                                 <  1:4928957/71‑1 (MQ=255)                                   tatTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATtgt                                 <  1:950509/71‑1 (MQ=255)                                   tatTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATtgt                                 <  1:758249/71‑1 (MQ=255)                                   tatTGTGCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATtgt                                 <  1:4323114/71‑1 (MQ=255)                                   tatTGTGCAGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATtgt                                 <  1:990010/71‑1 (MQ=255)                                    atTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATAtt                                   >  1:578876/1‑68 (MQ=255)                                    atTGTGCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATtgtg                                >  1:976222/1‑71 (MQ=255)                                     ttGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACaa                                                               <  1:1824098/39‑1 (MQ=255)                                     ttGTGCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTg                                         <  1:1129082/61‑1 (MQ=255)                                     ttGTGCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTg                                         <  1:2431211/61‑1 (MQ=255)                                       gtgCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCg                             >  1:442508/1‑71 (MQ=255)                                       gtgCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGaa                                       >  1:3478242/1‑61 (MQ=255)                                           cGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTa                         <  1:3257930/71‑1 (MQ=255)                                           cGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTa                         <  1:49313/71‑1 (MQ=255)                                           cGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTa                         <  1:3925667/71‑1 (MQ=255)                                             gTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAAc                                            >  1:1131987/1‑50 (MQ=255)                                             gTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAAc                                            >  1:1457477/1‑50 (MQ=255)                                             gTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAg                       <  1:3177544/71‑1 (MQ=255)                                              tAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGtt                          <  1:4820998/67‑1 (MQ=255)                                              tAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGtt                          <  1:1276332/67‑1 (MQ=255)                                              aaaaTATCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGtt                          <  1:1157293/66‑1 (MQ=255)                                               aaaTTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCaa                                             >  1:3275700/1‑47 (MQ=255)                                               aaaTTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAAGCTGAata                                     >  1:1678989/1‑55 (MQ=255)                                               aaaTTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGACATCGGCAACCTGAATATTGTGCCGGTTAAGTg                     >  1:2769619/1‑71 (MQ=255)                                                aaTTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGc                                               >  1:1515398/1‑44 (MQ=255)                                                aaTTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAAc                                            >  1:4427790/1‑47 (MQ=255)                                                 aTTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCa                                                    <  1:2698564/38‑1 (MQ=255)                                                 aTTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATAtt                                   <  1:2476260/55‑1 (MQ=255)                                                 aTTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAatat                                    <  1:4636607/54‑1 (MQ=255)                                                    tCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCa                                                    >  1:4708781/1‑35 (MQ=255)                                                     cTTTTTCCCCGCATCTAAAACAAATCTTGCGTCAt                                                   <  1:2882631/35‑1 (MQ=255)                                                        tttCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGaa                                       >  1:3577000/1‑44 (MQ=255)                                                        tttCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCa             <  1:3677220/70‑1 (MQ=255)                                                        tttCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGc                               >  1:4801769/1‑52 (MQ=255)                                                         ttCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCAt            <  1:3380851/70‑1 (MQ=255)                                                            cccGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTGAg        <  1:612140/71‑1 (MQ=255)                                                             ccGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTGAGc       <  1:2387516/71‑1 (MQ=255)                                                                cATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATAATTGAGCATc    >  1:914448/1‑71 (MQ=255)                                                                   ttAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTGAGCATCtt  >  1:4964182/1‑70 (MQ=255)                                                                   ttAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTGAGCATCtt  >  1:4403289/1‑70 (MQ=255)                                                                   |                                                                      TTTCTTCTTCGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTGAGCATCTT  >  W3110S.gb/3764598‑3764733

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: ‑