Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,989,559	G→A	7.5%	C117Y (TGC→TAC)	ygeF →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,989,559	0	G	A	7.5%	159.3 / 3.3	53	C117Y (TGC→TAC)	ygeF	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (27/22);  new base A (2/2);  total (29/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.60e-01

GCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACA  >  W3110S.gb/2989489‑2989616                                                                       |                                                          gCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATg                                                           >  1:468520/1‑71 (MQ=255)    gTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGca                                                         >  1:584191/1‑70 (MQ=255)            aCTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTc                                                <  1:1205600/71‑1 (MQ=255)            aCTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTc                                                <  1:3314038/71‑1 (MQ=255)               cATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTAt                                             >  1:1069915/1‑71 (MQ=255)               cATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTAt                                             >  1:178404/1‑71 (MQ=255)                aTAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGcaca                                                       >  1:1944137/1‑60 (MQ=255)                aTAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTa                                              >  1:1702621/1‑69 (MQ=255)                aTAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATc                                            <  1:1118307/71‑1 (MQ=255)                aTAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATc                                            >  1:259692/1‑71 (MQ=255)                aTAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATACACAGACGTTCTATc                                            >  1:3278479/1‑71 (MQ=255)                 tAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGt                                                  <  1:1529913/64‑1 (MQ=255)                  aaaaCTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACg                                                   <  1:2941017/62‑1 (MQ=255)                  aaaaCTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACg                                                   <  1:1555214/62‑1 (MQ=255)                  aaaaCTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATccc                                          >  1:1407749/1‑71 (MQ=255)                   aaaCTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGt                                                  >  1:4144392/1‑62 (MQ=255)                    aaCTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATccccc                                        <  1:2232599/71‑1 (MQ=255)                      cTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGa                                                     >  1:4438937/1‑56 (MQ=255)                          ccAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTc                                  <  1:165855/71‑1 (MQ=255)                           cAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTc                                  <  1:2020729/70‑1 (MQ=255)                             aaaTAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCAc                                >  1:518731/1‑70 (MQ=255)                             aaaTAGAGAATAATGTAGACCTGAATAAATTCACTACTATATACACAGACGTTCTa                                              >  1:3464657/1‑56 (MQ=255)                             aaaTAGAGAATAATGTAGACCTGAATAAATTCACTACTATATACACAGACGTTCTATCCCCCCGCGTCAc                                <  1:958314/70‑1 (MQ=255)                              aaTAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCAc                                >  1:336993/1‑69 (MQ=255)                                  gagaATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTa                                              >  1:1804312/1‑51 (MQ=255)                                   agaATAATGTAGACCTGAATAAATTCACTACTATATg                                                           <  1:2980899/37‑1 (MQ=255)                                       taatGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCACCAGACataat                      >  1:1882593/1‑70 (MQ=255)                                        aatGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTa                                              >  1:1726737/1‑45 (MQ=255)                                         atGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCACCAGACataata                     >  1:970992/1‑69 (MQ=255)                                         atGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCACCAGACAtaataa                    <  1:3387632/70‑1 (MQ=255)                                         atGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCACCAGACATAATaaa                   <  1:1694173/71‑1 (MQ=255)                                          tGTAGACCTGAATAAATTCACTACTATATACACAGACGTTCTATCCCCCCGCGTCACCAGACAtaataa                    <  1:2104776/69‑1 (MQ=255)                                             aGACCTGAATAAATTCACTACTATATGCACAGAGGTTCTATCCCCCCGCGTCACCAGACATAATAAAGaa                >  1:3478959/1‑70 (MQ=255)                                             aGACCTGAATAAATTCACTACTATATGCACAGACGTTCTAt                                             >  1:2114044/1‑41 (MQ=255)                                              gACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCACCAGACATAATAAAGaaa               >  1:3441491/1‑70 (MQ=255)                                               aCCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCa                                 >  1:1576544/1‑51 (MQ=255)                                               aCCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCACCAGACATAATAAAGaaaaa             <  1:634155/71‑1 (MQ=255)                                                ccTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCACCAGACATAATAAAGaaaaaa            <  1:1680181/71‑1 (MQ=255)                                                 cTGAATAAATTCACTACTATATGCACAGACGTTCTAt                                             >  1:849309/1‑37 (MQ=255)                                                    aaTAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCACCAGATATAATAAAGAAAAaaac          <  1:4174327/69‑1 (MQ=255)                                                    aaTAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCACCAGACATAATAAAGaa                <  1:616849/63‑1 (MQ=255)                                                     aTAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCACCAGACATAATAAAGAAAAaaacaaa       >  1:2398065/1‑71 (MQ=255)                                                     aTAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCACCAGACATAATAAAGAAAAaaacaaa       >  1:3213087/1‑71 (MQ=255)                                                     aTAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCACCAGACATAATAAAGAAAAaaacaaa       >  1:4595030/1‑71 (MQ=255)                                                     aTAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCACCAGACATAATAAAGAAAAaaacaaa       >  1:139638/1‑71 (MQ=255)                                                      tAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCACCAGACATAATAAAGAAAAaaacaaac      >  1:4332804/1‑71 (MQ=255)                                                       aaaTTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCACCAGACATAATAAAGAAAAaaaca         <  1:121567/67‑1 (MQ=255)                                                          ttCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCACCAg                             <  1:632582/44‑1 (MQ=255)                                                             actactATATGCACAGACGTTCTATCCCCCCGCGTCACCAGACATAATAAAGaaaaaa            >  1:3033043/1‑58 (MQ=255)                                                              ctactaTATGCACAGACGTTCTATCCCCCCGCGTCACCAGa                            <  1:3582950/41‑1 (MQ=255)                                                              ctactaTATGCACAGACGTTCTATCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACa  <  1:4388875/67‑1 (MQ=255)                                                                actaTATGCACAGACGTTCTATCCCCCCGCGTCACCAGACat                         <  1:1265508/42‑1 (MQ=255)                                                                    tatGCACAGACGTTCTATCCCCCCGCGTCACCAGACATAATAAAGAAAAaaaca         <  1:1263979/54‑1 (MQ=255)                                                                      tGCACAGACGTTCTATCCCCCCGCGTCACCAGACataata                     <  1:1430296/40‑1 (MQ=255)                                                                      tGCACAGACGTTCTATCCCCCCGCGTCACCAGACATAATAAAGAAAAaaacaaa       >  1:2615801/1‑54 (MQ=255)                                                                       |                                                          GCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACA  >  W3110S.gb/2989489‑2989616

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: ‑