Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	980,260	T→A	6.8%	E15D (GAA→GAT)	cspI ←	cold shock protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	980,260	0	T	A	6.8%	166.2 / 4.0	59	E15D (GAA→GAT)	cspI	cold shock protein
Reads supporting (aligned to +/- strand):  ref base T (21/34);  new base A (2/2);  total (23/36)
Fisher's exact test for biased strand distribution p-value = 6.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.19e-01

AATTGCTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTA  >  minE/980194‑980328                                                                   |                                                                     aaTTGCTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCGAAACCTTTTTc                                                                    <  1:2127203/69‑1 (MQ=255) aaTTGCTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTc                                                                    <  1:1026343/69‑1 (MQ=255) aaTTGCTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCa                                                                   <  1:642689/70‑1 (MQ=255)      cTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTa                                                             <  1:547626/71‑1 (MQ=255)        gagaAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTaaa                                                           >  1:256963/1‑71 (MQ=255)          gaAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAAc                                                          >  1:1501188/1‑70 (MQ=255)           aaaTAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAgg                                                                 >  1:1246287/1‑62 (MQ=255)             aTAGACAAACACATCTTTTCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCAtt                                                      <  1:2231721/71‑1 (MQ=255)             aTAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAgg                                                                 <  1:601740/60‑1 (MQ=255)             aTAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCAtt                                                      >  1:363315/1‑71 (MQ=255)             aTAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCAtt                                                      >  1:2115194/1‑71 (MQ=255)                gACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCa                                                   >  1:479987/1‑71 (MQ=255)                 aCAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCttttt                                                                     <  1:2791493/52‑1 (MQ=255)                 aCAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCttttt                                                                     <  1:2482070/52‑1 (MQ=255)                   aaaCACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTa                                                <  1:2727818/71‑1 (MQ=255)                   aaaCACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTa                                                <  1:2277477/71‑1 (MQ=255)                     acacATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTaaa                                              <  1:2227212/71‑1 (MQ=255)                      cacaTCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAc                                             <  1:3266168/71‑1 (MQ=255)                      cacaTCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAAc                                             >  1:1670177/1‑71 (MQ=255)                      cacaTCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAAc                                             >  1:2214762/1‑71 (MQ=255)                       acaTCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAc                                             >  1:68072/1‑70 (MQ=255)                       acaTCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAc                                             >  1:1952714/1‑70 (MQ=255)                       acaTCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAc                                             >  1:801449/1‑70 (MQ=255)                         aTCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAgg                                                                 <  1:1034334/48‑1 (MQ=255)                           cTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTa                                                <  1:3571749/63‑1 (MQ=255)                            tttGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAc                                             >  1:1066563/1‑65 (MQ=255)                             ttGCTGCCATCTTTCGGCGTGATGAAACCAAAACCttttt                                                                     >  1:1842473/1‑40 (MQ=255)                             ttGCTGCCATCTTTCGGCGTGATGAAACCAAAACCttttt                                                                     >  1:2823302/1‑40 (MQ=255)                             ttGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCa                                                   >  1:1605349/1‑58 (MQ=255)                              tgctgcCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGt                                         <  1:2879782/67‑1 (MQ=255)                                ctgcCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAtttt                                   <  1:841682/71‑1 (MQ=255)                                   ccATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAAc                                                          <  1:1463075/45‑1 (MQ=255)                                   ccATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                                 <  1:1004229/70‑1 (MQ=255)                                   ccATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                                 >  1:1378120/1‑70 (MQ=255)                                   ccATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                                 <  1:3508796/70‑1 (MQ=255)                                   ccATCTTTCGGCGTCATGAAACCAAAACCTTTTTCAGGGTTAAAc                                                          <  1:3410776/45‑1 (MQ=255)                                     aTCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAg                              <  1:2090371/71‑1 (MQ=255)                                      tCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAAc                                                          >  1:2238685/1‑42 (MQ=255)                                      tCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGa                             >  1:1199119/1‑71 (MQ=255)                                       cTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCa                                                        <  1:3114156/43‑1 (MQ=255)                                       cTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCa                                                        <  1:2309491/43‑1 (MQ=255)                                       cTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGa                             >  1:1120168/1‑70 (MQ=255)                                           cGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCAc                                                  >  1:22512/1‑45 (MQ=255)                                            ggCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTc                                                    <  1:2020739/42‑1 (MQ=255)                                            ggCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTc                                                    <  1:1717763/42‑1 (MQ=255)                                            ggCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTc                                                    <  1:1159330/42‑1 (MQ=255)                                             gagTGATAAAGCCAAAACCTTTATCTGCGTTAAACCATTTTACTAAACCAGTCATTTTATTAGACATAttt                      <  1:1639919/69‑1 (MQ=255)                                             gagTGATAAAGCCAAAACCTTTATCTGCGTTAAACCATTTTACTAAACCAGTCATTTTATTAGACATAttt                      <  1:3226215/69‑1 (MQ=255)                                             gCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAatt                      <  1:2358719/71‑1 (MQ=255)                                              cGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCAc                                                  >  1:628724/1‑42 (MQ=255)                                              cGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAatta                     <  1:1436152/71‑1 (MQ=255)                                               gTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAattat                    <  1:2450815/71‑1 (MQ=255)                                                    gaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAtttt                                   <  1:1065795/51‑1 (MQ=255)                                                    gaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAtttt                                   <  1:759609/51‑1 (MQ=255)                                                    gaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAtttt                                   <  1:3716857/51‑1 (MQ=255)                                                     aaaCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAatta                     <  1:2523530/64‑1 (MQ=255)                                                     aaaCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCtt              >  1:1085912/1‑71 (MQ=255)                                                      aaCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCtt              >  1:1945841/1‑70 (MQ=255)                                                           aaaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg           >  1:932530/1‑68 (MQ=255)                                                            aaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaag        >  1:3236980/1‑70 (MQ=255)                                                             aCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaagaa      <  1:1315181/71‑1 (MQ=255)                                                              ccTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg           <  1:2692405/65‑1 (MQ=255)                                                               cTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                                 <  1:514736/42‑1 (MQ=255)                                                                tttttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCtttt            <  1:763565/62‑1 (MQ=255)                                                                 ttttCAGGGTTAAACCATTTCACTAAACCAGTCAtttt                                   <  1:3532901/38‑1 (MQ=255)                                                                 ttttCAGGGTTAAACCATTTCACTAAACCAGTCAtttt                                   <  1:3455549/38‑1 (MQ=255)                                                                 ttttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTa                               >  1:1723033/1‑42 (MQ=255)                                                                 ttttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTa                               >  1:2921583/1‑42 (MQ=255)                                                                 ttttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCtttt            <  1:2428180/61‑1 (MQ=255)                                                                  tttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTa  <  1:2002147/70‑1 (MQ=255)                                                                  tttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAACAAATTa  <  1:6368/70‑1 (MQ=255)                                                                   |                                                                     AATTGCTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTA  >  minE/980194‑980328

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: ‑