Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	980,260	T→A	12.3%	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	12.3%	149.6 / 12.9	67	E15D (GAA→GAT)	cspI	cold shock protein
Reads supporting (aligned to +/- strand):  ref base T (28/28);  new base A (3/4);  total (31/36)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.72e-01

AATTGCTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAAT  >  minE/980194‑980326                                                                   |                                                                   aaTTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAg                                                                >  1:2917685/1‑71 (MQ=255) aaTTGCTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAg                                                                >  1:1779617/1‑71 (MQ=255)  aTTGCTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAgg                                                               >  1:1237321/1‑71 (MQ=255)  aTTGCTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAgg                                                               >  1:1634379/1‑71 (MQ=255)      cTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTa                                                           <  1:2521743/71‑1 (MQ=255)      cTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTa                                                           <  1:3571031/71‑1 (MQ=255)          gaAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAAc                                                        >  1:3664975/1‑70 (MQ=255)           aaaTGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCa                                                      >  1:1007396/1‑71 (MQ=255)            aaTGGACAAACACATCTTTGCTGCCATCTTTCGGAGTGATGAAACCAAAACCTTTTTCAg                                                                <  1:494509/60‑1 (MQ=25)             atggACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCAtt                                                    <  1:987032/68‑1 (MQ=255)              tggACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAggg                                                              >  1:1273661/3‑60 (MQ=255)              tggACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAggg                                                              >  1:232045/3‑60 (MQ=255)              tAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCAttt                                                   <  1:2211814/71‑1 (MQ=255)               gcaCAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCAttt                                                   >  1:2548954/3‑70 (MQ=255)                caCAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCAtttta                                                 <  1:658298/70‑3 (MQ=255)                  cAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCAc                                                >  1:1534400/1‑70 (MQ=255)                  cAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACt                                               <  1:1450160/71‑1 (MQ=255)                  cAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACt                                               <  1:2728011/71‑1 (MQ=255)                   aaaCACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTa                                              <  1:3525091/71‑1 (MQ=255)                    aaCACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTaa                                             <  1:1430417/71‑1 (MQ=255)                    aaCACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTaa                                             <  1:3226106/71‑1 (MQ=255)                     acacATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAggg                                                              >  1:2235155/1‑53 (MQ=255)                     acacATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTaaa                                            >  1:3760251/1‑71 (MQ=255)                       acgtCTTTGCTGCCATCATCAGGAGTGATAAAGCCAAAACCTTTATCTGCGTTAAACCATTTTACTAAAcc                                          <  1:2092435/68‑1 (MQ=9)                       acgtCTTTGCTGCCATCATCAGGAGTGATAAAGCCAAAACCTTTATCTGCGTTAAACCATTTTACTAAAc                                           >  1:3505348/4‑70 (MQ=9)                       acaTCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAcc                                          <  1:3379269/71‑1 (MQ=255)                               gctgcCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAttt                                  >  1:1066236/1‑71 (MQ=255)                               gctgcCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAtt                                   <  1:2909648/70‑1 (MQ=255)                                gagcCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATACCAGTCAtttt                                 <  1:3804793/69‑1 (MQ=255)                                gagcCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATACCAGTCAtttt                                 <  1:2536224/69‑1 (MQ=255)                                 tgcCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCAttt                                                   <  1:2182225/52‑1 (MQ=255)                                 tgcCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCAt                                                     <  1:531124/50‑1 (MQ=255)                                 agcCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATACCAGTCAtttt                                 <  1:2864534/69‑1 (MQ=255)                                   ccATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCAc                                                <  1:833754/53‑1 (MQ=255)                                   ccATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                               <  1:2761567/70‑1 (MQ=255)                                    cATCTTTCGGCGTGATGAAACCAAAACCTTTTTCa                                                                 <  1:3158695/35‑1 (MQ=255)                                    cATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTaa                                                          >  1:2866869/1‑42 (MQ=255)                                    cATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCa                                                 >  1:400185/1‑51 (MQ=255)                                    cATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTa                             <  1:1984849/71‑1 (MQ=255)                                     aTCTTTCGGCGTGATGAAACCAAAACCTTTTTCAg                                                                <  1:2663073/35‑1 (MQ=255)                                     aTCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAc                                           <  1:2536476/56‑1 (MQ=255)                                      tCTTTCGGCGTGATGAAACCAAAACCTTTTTCAgg                                                               <  1:1487346/35‑1 (MQ=255)                                      tCTTTCGGCGTGATGAAACCAAAACCTTTTTCAgg                                                               <  1:1740353/35‑1 (MQ=255)                                       cTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTg                                >  1:1881533/1‑65 (MQ=255)                                        tttCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAtt                                   >  1:3310296/1‑61 (MQ=255)                                        tttCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACa                         >  1:1521667/1‑71 (MQ=255)                                           ctgCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATa                       <  1:2200645/68‑1 (MQ=255)                                           cGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATaa                      >  1:3118615/1‑71 (MQ=255)                                           cGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATaa                      >  1:1203435/1‑71 (MQ=255)                                             gCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAtt                                   <  1:3418694/56‑1 (MQ=255)                                             gCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAatt                    <  1:3671569/71‑1 (MQ=255)                                              cGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAat                     <  1:3395416/69‑1 (MQ=255)                                              agTGATAAAGCCAAAACCTTTATCTGCGTTAAACCATTTTACTAAAc                                           >  1:825724/2‑47 (MQ=16)                                                    gaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                               >  1:3460537/1‑53 (MQ=255)                                                    gaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCt             >  1:2399905/1‑71 (MQ=255)                                                    gaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCt             >  1:3817724/1‑71 (MQ=255)                                                      aaCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCttt           >  1:3280759/1‑71 (MQ=255)                                                        ccAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg         <  1:800234/71‑1 (MQ=255)                                                        ccAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg         <  1:2936467/71‑1 (MQ=255)                                                        ccAAAACCTTTATCTGCGTTAAACCATTTTACTAAACCAGTCAtttt                                 <  1:1918042/47‑1 (MQ=255)                                                          aaaaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATGATTACCTTTTg         >  1:1369223/1‑69 (MQ=255)                                                           aaaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAttt                                  >  1:590728/1‑43 (MQ=255)                                                             aCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaaga     >  1:3047348/1‑70 (MQ=255)                                                             aCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaaga     >  1:769702/1‑70 (MQ=255)                                                             aCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaag      >  1:2201983/1‑69 (MQ=255)                                                               cTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAAt  <  1:2112271/71‑1 (MQ=255)                                                               cTTTGTCAGCGTTGAACCATTTTACGATACCAGTCAtttt                                 <  1:2318751/40‑1 (MQ=16)                                                                 ttttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg         >  1:3350166/1‑62 (MQ=255)                                                                 ttttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAAt  >  1:3311983/1‑69 (MQ=255)                                                                  tttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                               >  1:3499314/1‑39 (MQ=255)                                                                  tttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAattat                  >  1:2159221/1‑52 (MQ=255)                                                                   |                                                                   AATTGCTGAGAAATAGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAAT  >  minE/980194‑980326

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: ‑