Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	980,278	C→T	14.8%	V9V (GTG→GTA)	cspI ←	cold shock protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	980,278	0	C	T	14.8%	192.7 / 20.3	74	V9V (GTG→GTA)	cspI	cold shock protein
Reads supporting (aligned to +/- strand):  ref base C (32/31);  new base T (2/9);  total (34/40)
Fisher's exact test for biased strand distribution p-value = 5.53e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATGGTC  >  minE/980211‑980347                                                                    |                                                                      cAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCAc                                                                     >  1:1534400/1‑70 (MQ=255) cAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACt                                                                    <  1:2728011/71‑1 (MQ=255) cAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACt                                                                    <  1:1450160/71‑1 (MQ=255)  aaaCACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTa                                                                   <  1:3525091/71‑1 (MQ=255)   aaCACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTaa                                                                  <  1:3226106/71‑1 (MQ=255)   aaCACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTaa                                                                  <  1:1430417/71‑1 (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                                                      <  1:2536224/69‑1 (MQ=255)               gagcCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATACCAGTCAtttt                                                      <  1:3804793/69‑1 (MQ=255)                agcCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATACCAGTCAtttt                                                      <  1:2864534/69‑1 (MQ=255)                  ccATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCAc                                                                     <  1:833754/53‑1 (MQ=255)                  ccATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                                                    <  1:2761567/70‑1 (MQ=255)                   cATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCa                                                                      >  1:400185/1‑51 (MQ=255)                   cATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTa                                                  <  1:1984849/71‑1 (MQ=255)                    aTCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAc                                                                <  1:2536476/56‑1 (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                          >  1:769702/1‑70 (MQ=255)                                            aCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaaga                          >  1:3047348/1‑70 (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)                                                   tCAGCGTTAAACCATTTTACTAAACCAGTCATTTTATTTGACAtt                                            <  1:3601552/45‑2 (MQ=255)                                                    cAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGccc                 >  1:1412852/1‑71 (MQ=255)                                                    cAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGccc                 >  1:1707663/1‑71 (MQ=255)                                                    cAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGcc                  <  1:349227/70‑1 (MQ=255)                                                     aGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTa                                                  >  1:554007/1‑37 (MQ=255)                                                     aGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAAtt                      >  1:3329426/1‑65 (MQ=255)                                                     aGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGccc                 <  1:222247/70‑1 (MQ=255)                                                      gggTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCtt               <  1:726070/71‑1 (MQ=255)                                                      gggTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCtt               <  1:3305656/71‑1 (MQ=255)                                                      gggTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCtt               <  1:541404/71‑1 (MQ=255)                                                         ttAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAatt                                         <  1:3056771/42‑1 (MQ=255)                                                         ttAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTggg            >  1:2737401/1‑71 (MQ=255)                                                         ttAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTggg            >  1:480068/1‑71 (MQ=255)                                                          tAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAatt                                         <  1:2716530/41‑1 (MQ=255)                                                          tAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGc                   >  1:599499/1‑63 (MQ=255)                                                            aaCCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAg         <  1:2058300/71‑1 (MQ=255)                                                             aCCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTggg            >  1:130865/1‑67 (MQ=255)                                                              ccATTTTACTAAACCAGTCATTTTATTAGACATAtttt                                        <  1:641789/38‑2 (MQ=25)                                                              ccATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGaa       <  1:1168142/71‑1 (MQ=255)                                                              ccATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGaa       <  1:1934247/71‑1 (MQ=255)                                                              ccATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGaa       <  1:2647146/71‑1 (MQ=255)                                                                aTTTCACTAAACCAGTCATTTTGTTATACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATg     <  1:3279613/71‑1 (MQ=255)                                                                 tttCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATgg    <  1:522104/71‑1 (MQ=255)                                                                 tttCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATgg    <  1:2416290/71‑1 (MQ=255)                                                                   tCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGa        >  1:2227239/1‑65 (MQ=255)                                                                   tCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATGGTc  >  1:2714531/1‑71 (MQ=255)                                                                    cACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaa                            >  1:634468/1‑44 (MQ=255)                                                                    cACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTa                     >  1:2233963/1‑51 (MQ=255)                                                                    |                                                                      CAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATGGTC  >  minE/980211‑980347

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: ‑