Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,765,203	A→T	Q119L (CAG→CTG)	yibJ →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,765,203	0	A	T	98.6%	220.2 / ‑3.6	70	Q119L (CAG→CTG)	yibJ	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base T (26/43);  total (27/43)
Fisher's exact test for biased strand distribution p-value = 3.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.01e-01

CGCTATTATGACCCGCTGCAGGGGCGGTATATCACTCAGGATCCGATTGGGCTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGATC  >  NC_000913/3765184‑3765292                    |                                                                                           cGCTATTATGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCg                  <  1:6810999/93‑1 (MQ=9)  gCTATTATGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCgg                 >  1:1268648/1‑93 (MQ=12)  gCTATTATGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCgg                 >  1:8491401/1‑93 (MQ=12)  gCTATTATGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCgg                 >  1:1683869/1‑93 (MQ=12)  gCTATTATGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCgg                 >  2:1366176/1‑93 (MQ=12)  gCTATTATGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCgg                 >  2:4498160/1‑93 (MQ=12)  gCTATTATGACCCGCTGCAGGGGCGGTATATCACTCAGGATCCGATTGGGCTGAA‑GGGGGGATGGAAGTTTTATCAGTATCCGTTGAATcaag                 >  1:4179178/1‑90 (MQ=0)  ccTATTATGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCgg                 <  2:2638882/92‑1 (MQ=12)   cTATTATGACCCGCTGCTGGGGCGTTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGt                <  1:4967275/93‑1 (MQ=255)   cTATTATGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGt                <  1:2257760/93‑1 (MQ=255)   cTATTATGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGt                >  1:8411695/1‑93 (MQ=255)   cTATTATGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGt                <  1:8537660/93‑1 (MQ=16)   cTATTATGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGt                <  2:1073604/93‑1 (MQ=16)   cTATTATGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGt                >  1:4574087/1‑93 (MQ=16)   cTATTATGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGt                >  2:6667620/1‑93 (MQ=255)    tattatGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTc               >  1:3965477/1‑93 (MQ=255)    tattatGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTc               <  2:1227353/93‑1 (MQ=255)    tattatGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTc               <  2:5213220/93‑1 (MQ=255)    tattatGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTc               <  2:7019266/93‑1 (MQ=255)    tattatGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTc               >  1:1864850/1‑93 (MQ=255)    tattatGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTc               >  1:6876382/1‑93 (MQ=255)    tattatGACCCGCTGCTGGGGCAATATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTc               <  2:6293308/93‑1 (MQ=11)     attatGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCa              >  2:3882108/1‑93 (MQ=255)     attatGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCa              <  2:3785425/93‑1 (MQ=255)     attatGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCa              >  1:4088889/1‑93 (MQ=255)     attatGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCa              >  2:7009675/1‑93 (MQ=255)      ttatGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCAt             <  1:1253862/93‑1 (MQ=255)      ttatGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCAt             <  2:923032/93‑1 (MQ=255)      ttatGACCCGCTGCTGGGGCGGTATATCACCCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCAt             >  1:5379258/1‑93 (MQ=11)       tatGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATa            <  2:1723356/93‑1 (MQ=255)       tatGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCAGGTCATa            >  2:5114298/1‑93 (MQ=255)        atGCCCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATaa           <  2:596060/93‑1 (MQ=255)        atGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATaa           <  2:3216882/93‑1 (MQ=255)        atGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATaa           >  2:1913649/1‑93 (MQ=255)         tGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATaaa          >  1:1492168/1‑93 (MQ=255)         tGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATaaa          <  2:1774915/93‑1 (MQ=255)         tGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATaaa          <  2:6089095/93‑1 (MQ=255)         tGACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATaaa          <  1:3932668/93‑1 (MQ=255)          gACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGTTTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAAt         <  2:6618276/93‑1 (MQ=255)          gACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAAt         >  1:1199158/1‑93 (MQ=255)          gACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAAt         <  2:1680795/93‑1 (MQ=255)          gACCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAAt         <  1:5561501/93‑1 (MQ=255)           gcccGCTGCTGGGGCGGTATATCACTCAGGATCTGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATg        <  1:8569192/92‑1 (MQ=14)           aCCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATATATg        <  1:7614747/93‑1 (MQ=255)           aCCCGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATg        <  2:6277452/93‑1 (MQ=255)            cccGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGt       >  2:5429759/1‑93 (MQ=255)            cccGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGt       <  2:390555/93‑1 (MQ=255)            cccGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGt       <  2:6433315/93‑1 (MQ=255)            cccGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGt       <  2:1933345/93‑1 (MQ=255)            cccGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGt       <  2:3896983/93‑1 (MQ=255)             ccGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAAGGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGt       <  1:6865133/93‑1 (MQ=14)             ccGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTa      <  1:1702597/93‑1 (MQ=255)             ccGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTa      <  1:4271006/93‑1 (MQ=255)             ccGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTa      <  2:3323411/93‑1 (MQ=255)             ccGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTa      >  1:4380199/1‑93 (MQ=255)             ccGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTa      <  1:8680012/93‑1 (MQ=255)             ccGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTa      >  1:5684538/1‑93 (MQ=255)             ccGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTGTATCAGTATCCGTTGAATCCGGTCATAAATGTa      >  1:8509703/1‑93 (MQ=14)              cGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTaa     >  1:4262835/1‑92 (MQ=255)              cGCTGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAg     <  2:5080178/93‑1 (MQ=255)               gctgctGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAACTGTAgt    >  2:6056802/1‑92 (MQ=14)               gctgctGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGa    <  1:4792121/93‑1 (MQ=255)               gctgctGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGa    >  1:7431538/1‑93 (MQ=255)               gctgctGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGa    >  1:5908126/1‑93 (MQ=255)                ctgctgGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGAt   >  1:7174726/1‑93 (MQ=255)                ctgctgGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGAt   <  1:5895837/93‑1 (MQ=255)                cTGCGGGGGCGGTATATCTCTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGAt   <  1:621230/93‑1 (MQ=255)                 tGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGATc  <  1:7750470/93‑1 (MQ=255)                 tGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGATc  <  1:2860292/93‑1 (MQ=255)                 tGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGATc  <  1:7720465/93‑1 (MQ=255)                 tGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGATc  <  1:7720464/93‑1 (MQ=255)                 tGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGATc  <  1:1751382/93‑1 (MQ=255)                 tGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGATc  <  2:6742709/93‑1 (MQ=255)                 tGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGATc  <  2:6742710/93‑1 (MQ=255)                 tGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGATc  <  2:5563182/93‑1 (MQ=255)                 tGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGATc  >  2:8360262/1‑93 (MQ=255)                 tGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGATc  >  2:8514252/1‑93 (MQ=255)                 tGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGATc  <  2:8572023/93‑1 (MQ=255)                 tGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGATc  <  2:3048099/93‑1 (MQ=255)                 tGCTGGGGCGGTATATCACTCAGGATCCGATTGGACTGAA‑GGGGGGATGGAATTGTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGATc  <  1:3619218/93‑1 (MQ=255)                    |                                                                                           CGCTATTATGACCCGCTGCAGGGGCGGTATATCACTCAGGATCCGATTGGGCTGAA‑GGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCGGTCATAAATGTAGATC  >  NC_000913/3765184‑3765292

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑