Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,469,991	T→C	32.8%	S155G (AGC→GGC)	vacJ ←	predicted lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,469,991	0	T	C	32.8%	68.2 / 55.7	61	S155G (AGC→GGC)	vacJ	predicted lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (20/21);  new base C (10/10);  total (30/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.70e-01

CAGGAAAGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGACCAAGCGTACTACCGA  >  W3110S.gb/2469930‑2470056                                                              |                                                                  cAGGAAAGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGa                                                           <  1:765046/70‑1 (MQ=255)  aGGAAAGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAAc                                                         >  1:751205/1‑71 (MQ=255)     aaaGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCg                                                               >  1:1046935/1‑62 (MQ=255)      aaGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTa                                                     <  1:962957/71‑1 (MQ=255)      aaGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTa                                                     <  1:1413882/71‑1 (MQ=255)      aaGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACgg                                                       >  1:1435803/1‑69 (MQ=255)      aaGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGt                                                      >  1:2069593/1‑70 (MQ=255)       aGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTaa                                                    >  1:28628/1‑71 (MQ=255)         aaCCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACt                                                  >  1:591088/1‑71 (MQ=255)            cGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTAACTGaa                                               <  1:1360836/71‑1 (MQ=255)            cGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTAACTGaa                                               <  1:744684/71‑1 (MQ=255)               gTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGt                                            <  1:2428323/71‑1 (MQ=255)                tAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTaa                                                    >  1:247602/1‑62 (MQ=255)                  aaaaCCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTaa                                                    >  1:1938594/1‑60 (MQ=255)                  aaaaCCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGt                                            <  1:2751480/68‑1 (MQ=255)                  aaaaCCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTAACGTAg                                                            >  1:1127922/1‑52 (MQ=255)                    aaCCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTaa                                          >  1:1777934/1‑68 (MQ=255)                    aaCCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTaa                                          >  1:2431213/1‑68 (MQ=255)                         tCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATa                                  <  1:548511/71‑1 (MQ=255)                         tCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATa                                  <  1:2430680/71‑1 (MQ=255)                         tCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATa                                  <  1:1443344/71‑1 (MQ=255)                           cGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAAc                                >  1:1758099/1‑71 (MQ=255)                           cGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAAc                                >  1:457206/1‑71 (MQ=255)                            gCCATATCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATAAcc                               <  1:701452/71‑1 (MQ=255)                             ccATATCACCACCGTCATCACGCAGCGTGAAGCTAc                                                                 <  1:2191737/36‑1 (MQ=255)                             ccATATCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCAt                                   <  1:2458507/66‑1 (MQ=255)                              cATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCAt                                   <  1:1715072/65‑1 (MQ=255)                              cATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCAt                                   <  1:1101623/65‑1 (MQ=255)                               atatCACCACCGTCATCACGCAGCGTGAAGCTACCGTAg                                                            <  1:149500/39‑1 (MQ=255)                               atatCACCACCGTCATCACGCAGCGTGAAGCTACCGTAg                                                            <  1:610266/39‑1 (MQ=255)                               atatCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGcc                                      <  1:2444667/61‑1 (MQ=255)                                tatCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGt                                                      <  1:1574395/44‑1 (MQ=255)                                 atCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTaa                                                    >  1:1006320/1‑45 (MQ=255)                                  tCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTaa                                                    >  1:1712118/1‑44 (MQ=255)                                  tCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGc                          >  1:2718417/1‑70 (MQ=255)                                  tCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGc                          >  1:1717554/1‑70 (MQ=255)                                  tCACCACCGTCATCAAGCAGCGTGAAGCTACCGTAGaa                                                          >  1:256680/1‑38 (MQ=255)                                   caccacCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCa                        >  1:1919075/1‑71 (MQ=255)                                   caccacCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCa                        >  1:2617975/1‑71 (MQ=255)                                    accaccGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCa                        <  1:832298/70‑1 (MQ=255)                                    accaccGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCa                        >  1:51647/1‑70 (MQ=255)                                    accaccGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCa                        >  1:454717/1‑70 (MQ=255)                                    accaccGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCAt                       <  1:425128/71‑1 (MQ=255)                                    accaccGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCAt                       <  1:1944725/71‑1 (MQ=255)                                    accaccGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCAt                       <  1:2009260/71‑1 (MQ=255)                                    accaccGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTAACTGaa                                               >  1:2553204/1‑47 (MQ=255)                                       accGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGcc                                      >  1:1114041/1‑53 (MQ=255)                                         cGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATaa                                 >  1:2154971/1‑56 (MQ=255)                                           tcatcaCGCAGCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCAt                       <  1:143102/64‑1 (MQ=255)                                               caCGCAGCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGACCAAGc            >  1:848214/1‑71 (MQ=255)                                                aCGCAGCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGACCAAGCg           <  1:164872/71‑1 (MQ=255)                                                aCGCAGCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGACCAAGCg           >  1:919040/1‑71 (MQ=255)                                                     gCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCAt                       <  1:1117480/54‑1 (MQ=255)                                                     gCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCAt                       <  1:24568/54‑1 (MQ=255)                                                          aaGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGACCAAGCGTACTACCg   >  1:50355/1‑69 (MQ=255)                                                          aaGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGACCAAGCGTACTACCGa  <  1:1909874/70‑1 (MQ=255)                                                          aaGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATACCCCACGCCATAATGa                  >  1:1811860/1‑54 (MQ=255)                                                          aaGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGa                  >  1:2171288/1‑54 (MQ=255)                                                             cTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGACCAAGCg           <  1:1622119/58‑1 (MQ=255)                                                             cTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGACCAAGCg           <  1:2387703/58‑1 (MQ=255)                                                             cTACCGTAGAACGGTAACTGAACGTAAGACCCATAACCCACGCCATAATGACCAAGCg           <  1:1329687/58‑1 (MQ=255)                                                              |                                                                  CAGGAAAGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGACCAAGCGTACTACCGA  >  W3110S.gb/2469930‑2470056

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: ‑