Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	526,457	T→A	5.3%	F1325I (TTT→ATT)	rhsD →	rhsD element protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	526,457	0	T	A	5.3%	201.0 / 3.5	75	F1325I (TTT→ATT)	rhsD	rhsD element protein
Reads supporting (aligned to +/- strand):  ref base T (24/47);  new base A (2/2);  total (26/49)
Fisher's exact test for biased strand distribution p-value = 6.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.85e-01

AGAATAGATCTCTATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTGAAAAGAAAATGTCC  >  W3110S.gb/526389‑526521                                                                     |                                                                 aGAATAGATCTCTATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATAtttt                                                                >  1:3615813/1‑71 (MQ=255)  gAATAGATCTCTATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATAtttt                                                                <  1:3924222/70‑1 (MQ=255)  gAATAGATCTCTATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTg                                                               >  1:2813120/1‑71 (MQ=255)  gAATAGATCTCTATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTg                                                               >  1:3327184/1‑71 (MQ=255)   aaTAGATCTCTATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGc                                                              <  1:393565/71‑1 (MQ=255)    aTAGATCTCTATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATAttt                                                                 >  1:69213/1‑67 (MQ=255)       gATCTCTATGTAATGATATGGAATACTCTCGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCt                                                          <  1:4323603/71‑1 (MQ=255)         tctcTATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGc                                                              <  1:2560358/65‑1 (MQ=255)             tATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAgg                                                      >  1:1605205/1‑69 (MQ=255)             tATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAg                                                       <  1:1282843/68‑1 (MQ=255)                  aaTGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCAt                                                            >  1:2868101/1‑58 (MQ=255)                     gATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGaaa                                                >  1:3343014/1‑67 (MQ=255)                      atatGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTg                                                               <  1:4242126/51‑1 (MQ=255)                      atatGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTg                                                               <  1:2646147/51‑1 (MQ=255)                      atatGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTg                                                               <  1:4331372/51‑1 (MQ=255)                      atatGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTg                                                               <  1:880704/51‑1 (MQ=255)                         tGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGc                                                              <  1:47870/49‑1 (MQ=255)                         tGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGc                                                              <  1:3510445/49‑1 (MQ=255)                           gAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAAttt                                      <  1:2564527/71‑1 (MQ=255)                              tACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATc                                                           <  1:3445719/47‑1 (MQ=255)                              tACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATc                                                           <  1:2142294/47‑1 (MQ=255)                              tACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATc                                                           <  1:865961/47‑1 (MQ=255)                              tACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAg                                   <  1:4058908/71‑1 (MQ=255)                                ctctGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATaa                                         >  1:3738492/1‑63 (MQ=255)                                ctctGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGa                                  >  1:1068845/1‑70 (MQ=255)                                 tctGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGa                                                  <  1:949472/53‑1 (MQ=255)                                   tGGTATTGTCTGTAAAGATACTAATGGAAAATAttt                                                                 <  1:3158570/36‑1 (MQ=255)                                   tGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGaaa                                <  1:2734488/69‑1 (MQ=255)                                   tGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAg                               >  1:2538062/1‑70 (MQ=255)                                     gTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAg                               <  1:2502186/68‑1 (MQ=255)                                     gTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAg                               <  1:3908925/68‑1 (MQ=255)                                     gTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAg                               <  1:2686905/68‑1 (MQ=255)                                     gTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAg                            <  1:449880/71‑1 (MQ=255)                                     gTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAg                            <  1:3088916/71‑1 (MQ=255)                                      tATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACt                                              <  1:393547/52‑1 (MQ=255)                                       aTTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGt                           >  1:1425101/1‑70 (MQ=255)                                        ttGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCa                         >  1:2818863/1‑71 (MQ=255)                                        ttGGCTGTGTAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCa                         >  1:464645/1‑71 (MQ=255)                                          gTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAAtt                                       <  1:1983204/55‑1 (MQ=255)                                          gTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCata                       >  1:55340/1‑71 (MQ=255)                                          gTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCata                       >  1:28041/1‑71 (MQ=255)                                          gTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCat                        <  1:2545827/70‑1 (MQ=255)                                          gTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGACat                        <  1:1191184/70‑1 (MQ=255)                                             tGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATcc                    >  1:1602698/1‑71 (MQ=255)                                             tGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAAATGATAATTTAAGAAAGGAGTCATATcc                    >  1:1966297/1‑71 (MQ=255)                                              gTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAg                               <  1:1999277/59‑1 (MQ=255)                                               tAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCatat                      >  1:1006205/1‑67 (MQ=255)                                               tAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATctcctc                  <  1:3632793/71‑1 (MQ=255)                                                aaaGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGa                                  <  1:2675050/54‑1 (MQ=255)                                                aaaGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTGATATCctct                 >  1:412209/1‑71 (MQ=255)                                                 aaGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCctct                 >  1:2478904/1‑70 (MQ=255)                                                    aTACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGa                                  <  1:2503544/50‑1 (MQ=255)                                                     tACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAg                               <  1:1119745/52‑1 (MQ=255)                                                      aCTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGaa                                 <  1:1098538/49‑1 (MQ=255)                                                      aCTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCat                        >  1:3106849/1‑58 (MQ=255)                                                      aCTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCat                        >  1:643477/1‑58 (MQ=255)                                                      aCTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTgaa              >  1:424515/1‑68 (MQ=255)                                                       cTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGa                                  <  1:1765550/47‑1 (MQ=255)                                                       cTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTgaatag           <  1:2989862/70‑1 (MQ=255)                                                        tAATGGAAAATATATTGCATCTAAGGCAGAAACTGATAAtt                                       <  1:2987512/41‑1 (MQ=255)                                                        tAATGGAAAATATATTGCATCTAAGGCAGAAACTGATAAtt                                       <  1:2405910/41‑1 (MQ=255)                                                         aaTGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTgaaaagaa         >  1:2312910/1‑70 (MQ=255)                                                         aaTGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTgaaaagaa         >  1:2774755/1‑70 (MQ=255)                                                          aTGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGa                                  <  1:4041596/44‑1 (MQ=255)                                                          aTGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTgaaaagaaa        <  1:2245646/70‑1 (MQ=255)                                                          aTGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTgaaaagaa         <  1:1717970/69‑1 (MQ=255)                                                          aTGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTgaaaagaa         <  1:911312/69‑1 (MQ=255)                                                          aTGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTgaaaagaa         <  1:2989111/69‑1 (MQ=255)                                                          aTGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTgaaaagaa         <  1:1411427/69‑1 (MQ=255)                                                          aTGGAAAATATATTGCATCTAAGGCAGAAACTGATAATTTa                                     >  1:2311592/1‑41 (MQ=255)                                                          aTGGAAAATATATTGCATCTAAGGCAGAAACTGATAATTTa                                     >  1:1541105/1‑41 (MQ=255)                                                           tGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGa                                  <  1:772559/43‑1 (MQ=255)                                                           tGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAg                               <  1:1501308/46‑1 (MQ=255)                                                             gAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGaaa                                >  1:3841603/1‑43 (MQ=255)                                                               aaaTATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAg                               <  1:3141222/42‑1 (MQ=255)                                                               aaaTATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTGAAAAGAAAATGTcc  <  1:2262372/71‑1 (MQ=255)                                                                aaTATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAg                               <  1:4333852/41‑1 (MQ=255)                                                                aaTATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCa                         <  1:2350146/47‑1 (MQ=255)                                                                 atatTTTGCATCTAAGGCAGAAACTGATAATTTAAGaa                                 <  1:2882733/38‑1 (MQ=255)                                                                    ttttGCATCTAAGGCATAAACTGATAATTTAAGAAAGGAGTCATATCCTCTgaaaagaaaa       >  1:1964542/1‑61 (MQ=255)                                                                    ttttGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTgaaaagaaaa       >  1:2730744/1‑61 (MQ=255)                                                                     |                                                                 AGAATAGATCTCTATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAGGCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTGAAAAGAAAATGTCC  >  W3110S.gb/526389‑526521

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: ‑