Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	980,260	T→A	6.3%	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	6.3%	225.5 / 6.4	79	E15D (GAA→GAT)	cspI	cold shock protein
Reads supporting (aligned to +/- strand):  ref base T (37/37);  new base A (3/2);  total (40/39)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.20e-01

TGAATTGCTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAG  >  minE/980192‑980329                                                                     |                                                                      tGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCttttt                                                                      >  1:831058/1‑70 (MQ=255) tGAATTGCTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCtttt                                                                       <  1:1909561/69‑1 (MQ=255)  gAATTGCTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCttttt                                                                      >  1:2104409/1‑69 (MQ=255)   aaTTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAg                                                                   >  1:3376469/1‑71 (MQ=255)   aaTTGCTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTc                                                                     <  1:2260311/69‑1 (MQ=255)   aaTTGCTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTc                                                                     <  1:166648/69‑1 (MQ=255)   aaTTGCTGAGAAATAGAAAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAg                                                                   >  1:1303568/1‑71 (MQ=255)    aTTGCTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAgg                                                                  >  1:3111000/1‑71 (MQ=255)        cTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGtt                                                               <  1:3483792/70‑1 (MQ=255)         tGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTc                                                                     <  1:1210051/63‑1 (MQ=255)          gagaAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTaaa                                                            >  1:2814006/1‑71 (MQ=255)             aaaTAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCa                                                                    <  1:3005820/60‑1 (MQ=255)             aaaTAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCa                                                                    <  1:3001028/60‑1 (MQ=255)              aaTAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCa                                                                    >  1:3921384/1‑59 (MQ=255)              aaTAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCAt                                                        >  1:1910277/1‑71 (MQ=255)                tAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCAttt                                                      <  1:656965/71‑1 (MQ=255)                  gACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCa                                                    >  1:3146072/1‑71 (MQ=255)                   aCAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGt                                                                >  1:232536/1‑58 (MQ=255)                   aCAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCAtttt                                                     <  1:2770728/69‑2 (MQ=255)                     aaaCACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCa                                                                    >  1:681447/1‑52 (MQ=255)                     aaaCACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCa                                                                    >  1:1616963/1‑52 (MQ=255)                     aaaCACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCa                                                                    >  1:2651381/1‑52 (MQ=255)                     aaaCACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCa                                                                    >  1:1036952/1‑52 (MQ=255)                     aaaCACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAAc                                                           <  1:2570456/61‑1 (MQ=255)                     aaaCACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACt                                                  >  1:304054/1‑70 (MQ=255)                       acacATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTaaa                                               <  1:3288749/71‑1 (MQ=255)                        cacaTCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAc                                              >  1:3043582/1‑71 (MQ=255)                          caTCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAc                                              >  1:3386561/1‑69 (MQ=255)                           gtCTTTGCTGCCATCATCAGGAGTGATAAAGCCAAAACCTTTATCTGCGTTAAACCATTTTACTAAACCAg                                           >  1:2390159/2‑71 (MQ=9)                              tttGCTGCCATCTTTCGGCGTGATGAAACCAAAACCtttt                                                                       >  1:3404931/1‑40 (MQ=255)                              tttGCTGCCATCATCAGGAGTGATAAAGCCAAAACCTTTATCTGCGTTAAACCATTTTACTAAACCAGTCa                                        >  1:1965061/1‑71 (MQ=12)                                tgctgcCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAggg                                                                 >  1:472922/1‑44 (MQ=255)                                tgctgcCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCa                                                    >  1:43453/1‑57 (MQ=255)                                tgctgcCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGt                                          <  1:3571953/67‑1 (MQ=255)                                tgctgcCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAt                                       >  1:566309/1‑70 (MQ=255)                                     ccATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                                  <  1:1421616/70‑1 (MQ=255)                                        tCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTc                                                     <  1:2476967/48‑1 (MQ=255)                                        tCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAc                                              >  1:3936028/1‑55 (MQ=255)                                          tttCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCAc                                                   >  1:3815115/1‑48 (MQ=255)                                          tttCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAt                                       <  1:3776268/60‑1 (MQ=255)                                          tttCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTa                                >  1:2373808/1‑67 (MQ=255)                                            tCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGa                              <  1:282312/67‑1 (MQ=255)                                            tCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACAt                           <  1:1702742/70‑1 (MQ=255)                                            tCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACAt                           <  1:1131223/70‑1 (MQ=255)                                            tCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACAt                           <  1:1899011/70‑1 (MQ=255)                                             cGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGa                              <  1:2707690/66‑1 (MQ=255)                                              ggCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAat                        <  1:3668892/71‑1 (MQ=255)                                               gagTGATAAAGCCAAAACCTTTATCTGCGTTAAACCATTTTACTAAACCAGTCATTTTATTAGACATAttt                       <  1:3732265/69‑1 (MQ=255)                                               gCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAat                        <  1:2375025/70‑1 (MQ=255)                                               gCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAat                        >  1:1403659/1‑70 (MQ=255)                                                  tgatgaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                                  <  1:1443865/57‑1 (MQ=255)                                                   gatgaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAg                               <  1:141036/59‑1 (MQ=255)                                                    atgaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAACCCAGTCATTTTGTTAGACATAATTATTAc                  >  1:1118278/1‑71 (MQ=255)                                                    atgaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTc                                         >  1:2430700/1‑48 (MQ=255)                                                    atgaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTAc                  >  1:2435792/1‑71 (MQ=255)                                                    atgaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTAc                  >  1:681991/1‑71 (MQ=255)                                                    atgaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTAc                  >  1:1791914/1‑71 (MQ=255)                                                    atgaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTAc                  >  1:3689580/1‑71 (MQ=255)                                                       aaaCCAAAACCTTTTTCAGGGTTAAACCATTTCACTaaa                                               <  1:2146255/39‑1 (MQ=255)                                                       aaaCCAAAACCTTTTTCAGGGTTAAACCATTTCACTa                                                 <  1:1102343/37‑1 (MQ=255)                                                       aaaCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                                  >  1:3279076/1‑52 (MQ=255)                                                       aaaCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCtt               <  1:3966583/71‑1 (MQ=255)                                                        aaCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGAc                             >  1:3125964/1‑56 (MQ=255)                                                        aaCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCttt              <  1:2234344/71‑1 (MQ=255)                                                         aCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGAc                             >  1:3450140/1‑55 (MQ=255)                                                         aCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGAc                             >  1:1521040/1‑55 (MQ=255)                                                         aCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGAGATAATTATTACCtttt             >  1:3562023/1‑71 (MQ=255)                                                         aCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAatt                       <  1:275604/61‑1 (MQ=255)                                                         aCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCtttt             <  1:1097479/71‑1 (MQ=255)                                                         aCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCtttt             <  1:2667077/71‑1 (MQ=255)                                                         aCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCtttt             <  1:2858166/71‑1 (MQ=255)                                                          ccAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAtttt                                    <  1:3474137/47‑1 (MQ=255)                                                          ccAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAACAGTCAtttt                                    >  1:1181557/1‑47 (MQ=255)                                                             aaaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTg                                   <  1:1747438/45‑1 (MQ=255)                                                              aaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaaga        <  1:2374128/71‑1 (MQ=255)                                                              aaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaaga        <  1:1520341/71‑1 (MQ=255)                                                               aCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAatta                      >  1:3751185/1‑56 (MQ=255)                                                               aCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaagaa       <  1:224202/71‑1 (MQ=255)                                                               aCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaaga        >  1:2403280/1‑70 (MQ=255)                                                               aCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaag         >  1:2613212/1‑69 (MQ=255)                                                                ccTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAatta                      >  1:1797803/1‑55 (MQ=255)                                                                 cTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAt                                       <  1:59532/37‑1 (MQ=255)                                                                 cTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAAt     <  1:3350055/71‑1 (MQ=255)                                                                  tttttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                                  <  1:3269716/41‑1 (MQ=255)                                                                  tttttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaag         <  1:681908/66‑1 (MQ=255)                                                                  tttatCAGCGTTAAACCATTTTACTAAACCAGTCATTTTATTTGa                              <  1:4067809/45‑1 (MQ=255)                                                                   ttttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAAt     >  1:1281556/1‑69 (MQ=255)                                                                    tttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAAtt    <  1:3362705/69‑1 (MQ=255)                                                                    tttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAg  >  1:909849/1‑71 (MQ=255)                                                                     |                                                                      TGAATTGCTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAG  >  minE/980192‑980329

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: ‑