Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,096,810	A→G	noncoding (66/88 nt)	serX ←	tRNA‑Ser

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,096,810	0	A	G	98.3%	160.3 / ‑4.2	59	noncoding (66/88 nt)	serX	tRNA‑Ser
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base G (43/14);  total (45/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.77e-01

ATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑ACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGG  >  NC_000913/1096722‑1096899                                                                                           |                                                                                          aTCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑Gcccc                                                                                       <  1:1941988/93‑1 (MQ=25)  tCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGTTCGA‑Ggcccc                                                                                      >  2:1703655/1‑93 (MQ=255)  tCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGTTCGA‑Gccccc                                                                                      >  2:2258227/1‑93 (MQ=255)  tCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGCTTCGA‑Gccccc                                                                                      >  2:2258226/1‑93 (MQ=255)  tCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑Gccccc                                                                                      >  2:1022800/1‑93 (MQ=37)   ccccccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCg                                                                                     >  1:3901887/1‑93 (MQ=255)     ccccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGTTCGA‑GCCCCCGAt                                                                                   >  1:3049221/1‑93 (MQ=255)     ccccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGAt                                                                                   >  2:1174461/1‑93 (MQ=255)     ccccGGTGTGTGCAATATACGAAAAAAAAACCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGGGA‑GGGGGGGGTTCGA‑GGCCCCGAt                                                                                   >  2:336897/1‑93 (MQ=11)      cccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATa                                                                                  >  1:4510541/1‑93 (MQ=255)         ggTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTAGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGt                                                                               >  2:1132378/1‑93 (MQ=255)           tgtgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCTA‑GCCCCCGACACGTTg                                                                             >  2:1661653/1‑93 (MQ=255)            gtgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGTTCGA‑GCCCCCGATACGTTGc                                                                            >  2:4342602/1‑93 (MQ=255)            gtgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGc                                                                            <  1:2792981/93‑1 (MQ=255)             tgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGcc                                                                           >  1:917897/1‑93 (MQ=255)             tgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGcc                                                                           >  1:1313261/1‑93 (MQ=255)             tgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGAATCGA‑GCCCCCGATACGATGcc                                                                           >  2:621292/1‑93 (MQ=255)              gtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGGTACGTTGCCg                                                                          >  2:1578459/1‑93 (MQ=255)                  aaTATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTTGA‑GCCCCCGATATGTTGCCGtata                                                                      >  1:4045017/1‑93 (MQ=255)                   atatACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGTTCGA‑GGCCCCCCTACGCTGCCGCATac                                                                     >  2:127743/1‑93 (MQ=14)                   atatACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GGCCCCGATAAGTTGGCGTATac                                                                     >  1:3552726/1‑93 (MQ=14)                   atatACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATac                                                                     >  1:3552727/1‑93 (MQ=255)                   atatACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATac                                                                     >  2:127740/1‑93 (MQ=255)                    tataCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GGCCCCGATACGTTGCCGTATaca                                                                    >  2:2686286/1‑93 (MQ=255)                    tataCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GACCCCGATACGTTGCCGTTTaca                                                                    >  2:710592/1‑93 (MQ=255)                      taCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTATATATGGCGGTGA‑GGGGGGGATTCGA‑GACCCCGATACGTTGCCGGATacacc                                                                  >  2:2768915/1‑92 (MQ=14)                      taCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGCTACGTTGCCGTATacaca                                                                  >  1:2907830/1‑93 (MQ=255)                      taCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATacaaa                                                                  >  2:2658094/1‑91 (MQ=255)                        cGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACt                                                                >  1:1118746/1‑93 (MQ=255)                         gAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACtt                                                               >  2:601400/1‑93 (MQ=37)                         gAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACtt                                                               >  1:3330785/1‑93 (MQ=255)                           aaaaaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTc                                                             >  2:1172720/1‑93 (MQ=255)                           aaaaaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTc                                                             >  2:1926676/1‑93 (MQ=255)                           aaaaaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTc                                                             <  2:1952044/93‑1 (MQ=37)                            aaaaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTcc                                                            >  2:10755/1‑93 (MQ=255)                             aaaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGGCGTATACACACCTTGCa                                                           >  1:3070682/1‑93 (MQ=11)                             aaaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCa                                                           <  1:2335515/93‑1 (MQ=37)                              aaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAg                                                          <  1:1434579/93‑1 (MQ=37)                                aaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGc                                                        >  2:1866655/1‑93 (MQ=37)                                 aGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCATGc                                                        >  1:687691/1‑93 (MQ=11)                                  gCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑ACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGt                                                      >  2:1594368/1‑93 (MQ=37)                                   cccGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTg                                                     >  2:1462052/1‑93 (MQ=25)                                    ccGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGc                                                    >  1:618697/1‑93 (MQ=21)                                    ccGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGc                                                    >  1:4362092/1‑93 (MQ=21)                                    ccGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGc                                                    >  2:1981392/1‑93 (MQ=21)                                    ccGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCACCCGATACGTTCCCGTAAGCACCGTTTCCAAGCGTgt                                                    >  1:1421989/1‑92 (MQ=11)                                     cGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACAATTTCCAGGAGTGcc                                                   >  1:615157/1‑92 (MQ=11)                                      gTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATATACACTTTCCATGCGTGCTc                                                  >  1:4493437/1‑93 (MQ=255)                                      gTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCACGCGTGCTc                                                  >  2:165000/1‑93 (MQ=12)                                       tACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTCGA‑GCCCCCGATACGGTGCCGTATACACACTTTCCAGGCGTGCTc                                                  >  1:3833247/1‑93 (MQ=11)                                       tACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGAGCCCCCCGAAAGGTCGCCTTATACACACTTTCCATGCctcctc                                                  >  1:1026026/1‑93 (MQ=11)                                       tACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACCAAATTTCCCGGGGTGCTcc                                                 >  1:1026027/1‑93 (MQ=11)                                       tACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTcc                                                 >  1:1984240/1‑93 (MQ=14)                                       tACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTcc                                                 <  2:2452084/93‑1 (MQ=14)                                       tACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTcc                                                 <  1:3012597/93‑1 (MQ=14)                                       tACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTcc                                                 <  1:3012598/93‑1 (MQ=14)                                       tACTTTCGTACAAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGTTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTcc                                                 >  2:3258157/1‑93 (MQ=255)                                                                       ggTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCg                 <  1:1628930/93‑1 (MQ=17)                                                                       ggTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCg                 >  2:2352391/1‑93 (MQ=17)                                                                       ggTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCg                 >  1:368719/1‑93 (MQ=17)                                                                        gTGA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGt                <  2:1949107/93‑1 (MQ=18)                                                                         ggA‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGtt               <  2:3702043/92‑1 (MQ=21)                                                                           a‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTcc             >  2:4680959/1‑93 (MQ=37)                                                                           a‑GGGGGGGATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTcc             >  1:1955744/1‑93 (MQ=37)                                                                             gggggggATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCt            <  1:3671542/93‑1 (MQ=255)                                                                             gggggggATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCt            >  2:855411/1‑93 (MQ=255)                                                                               gggggATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGt          <  2:4068330/93‑1 (MQ=255)                                                                               gggggATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGt          >  1:2221406/1‑93 (MQ=255)                                                                                ggggATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTc         >  2:994916/1‑93 (MQ=255)                                                                                ggggATTCGA‑GCACCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTCTCGTTCCTGTc         >  1:753467/1‑93 (MQ=14)                                                                                 gggATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCt        >  1:2291845/1‑93 (MQ=255)                                                                                 gggATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCt        >  1:3554392/1‑93 (MQ=255)                                                                                 gggATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCt        >  2:1625184/1‑93 (MQ=255)                                                                                  ggATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCtt       <  2:2851230/93‑1 (MQ=255)                                                                                  ggATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCtt       >  1:2407548/1‑93 (MQ=255)                                                                                  ggATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCtt       <  1:306086/93‑1 (MQ=255)                                                                                   gATTCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTg      >  2:3976305/1‑93 (MQ=255)                                                                                     ttCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCt    >  1:3046721/1‑93 (MQ=255)                                                                                     ttCGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCt    >  2:4577538/1‑93 (MQ=255)                                                                                       cGA‑GCCCCCGATACGTTGCCGTATACTCACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTgg  <  1:1408037/93‑1 (MQ=255)                                                                                       cGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTgg  >  2:2449574/1‑93 (MQ=255)                                                                                       cGA‑GCCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTgg  <  1:1408034/93‑1 (MQ=255)                                                                                           |                                                                                          ATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGA‑ACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGG  >  NC_000913/1096722‑1096899

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑