Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,097,581	0	A	G	42.9%	79.8 / 16.5	50	noncoding (72/88 nt)	serX	tRNA‑Ser
Reads supporting (aligned to +/- strand):  ref base A (3/25);  new base G (21/0);  total (25/25)
Fisher's exact test for biased strand distribution p-value = 5.18e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAA  >  NC_000913/1097441‑1097730                                                                                                                                             |                                                                                                                                                       cGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAAccc                                                                                                                                               <  1:182482/150‑1 (MQ=34)      aCGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGGGAGGGGGGGGTTTGAAccccc                                                                                                                                             >  2:1375247/1‑147 (MQ=16)       cGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATa                                                                                                                                         <  1:1172861/150‑1 (MQ=39)           cTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGGTTGGAccccccgcacggt                                                                                                                                     >  1:1290103/1‑142 (MQ=1)               ccAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTTGAAACCCCCCTACGt                                                                                                                                      >  1:502637/1‑145 (MQ=11)               ccAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCg                                                                                                                                 <  1:539495/150‑1 (MQ=255)                     ggCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATacac                                                                                                                          <  2:1110703/151‑1 (MQ=255)                       cTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATCGCACCCCCCCTTCGTTTCCGtct                                                                                                                              >  1:337088/1‑143 (MQ=11)                         gTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACt                                                                                                                      <  1:999821/150‑1 (MQ=255)                           cGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTc                                                                                                                   <  2:540815/151‑1 (MQ=255)                            gCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGAGAGGGGGGGGGGTGGACCCCCCATACGATCACCTTTACAC‑ACttt                                                                                                                    >  1:1418801/1‑149 (MQ=11)                              cAGTTGTCGAACCCAGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAg                                                                                                                <  2:739620/151‑1 (MQ=255)                                gTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGc                                                                                                              <  2:137259/151‑1 (MQ=255)                                     cGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAAACCCCCATACGTTGCCGTATACAC‑ACTTTTCAGGCg                                                                                                             >  2:1085782/1‑147 (MQ=255)                                      gAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAACCCCCCATACGTTGCCGTATACAC‑ACTTTTCAGGCg                                                                                                             >  2:1075050/1‑146 (MQ=255)                                          cccGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGAGAGGGGGGGGTTCGAAACCCCCATACGTTGCCGTATACAC‑ACTTTTCAGGCGGGGTCCtt                                                                                                     >  1:66727/1‑150 (MQ=17)                                             ggTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGTTTGTACCCCCCAGACCTTTGCCTATATACAACTTTcccgcgcgtccctcct                                                                                                    >  1:784620/1‑135 (MQ=11)                                             ggTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTAGAAACCCCGCTTAGTTTCCGGATAAAC‑ACATTCCCAGGGGGCTCCCTCAGc                                                                                                 >  1:1358557/1‑151 (MQ=11)                                                           aTCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTc                                                                                   <  1:433835/151‑1 (MQ=255)                                                              cccccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGAGAGGGGGGGGTTTGAACCCCCCCTACGTTGCCGTATAAAC‑AATTTCCCGGGGTGGTCCTTCTGCCCCCCGGGCACCTCAcc                                                                                >  1:426622/1‑151 (MQ=17)                                                                     tgtgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGAAACCCCCCTACGTTTCCGTATACAC‑ACTTTCCAGGCGGGGTCCCTCCGCCCCCCCGACAccccccccaaattt                                                                         >  1:186761/1‑139 (MQ=14)                                                                      gtgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGt                                                                         <  2:1306257/150‑1 (MQ=255)                                                                      gtgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGGGAGGGGGGGGTTTTAAACCCCCCTACGTTGCCGTATACAC‑ACTTTTCAGGCGGGGTCCTTCTACCCCTCCGGCACCCCACCAAAATGt                                                                         >  1:434875/1‑150 (MQ=14)                                                                       tgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAAACCCCCATACGTTGCCGGATACAC‑ACTTTTCAGGCGGGGTCCTTTAGCCACTCCGGCACCCCACCaaa                                                                             >  2:571909/1‑145 (MQ=14)                                                                       tgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGAGAGGGGGGGGTTCGAACCCCCCCTAAATTTCCGTATACAC‑ACCTTCCAGGGGGGCTCCTTCCGCCCCCCGGGCACCCCCCCCAATTGt                                                                         >  1:724494/1‑149 (MQ=14)                                                                         tgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGt                                                                      <  1:870218/150‑1 (MQ=255)                                                                              tataCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAACCCCCCCTACGTTGCCGTATACAC‑ACTTTTCAGGCGTGCTCCCTCCGCCACTCGGGCACCCCCCCCAAATTTCGtt                                                                     >  2:827559/1‑146 (MQ=11)                                                                                     aaaaaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTg                                                         <  1:391986/151‑1 (MQ=255)                                                                                      aaaaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTgg                                                        <  1:1338578/151‑1 (MQ=255)                                                                                      aaaaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTCTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTgg                                                        <  1:208867/151‑1 (MQ=255)                                                                                         aaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAAc                                                     <  2:617460/151‑1 (MQ=255)                                                                                          aaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAATCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACg                                                    <  2:903359/151‑1 (MQ=255)                                                                                               cGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGAAACCCCCCTAAGTTGGCGGATACAC‑ACCTTCCAGGCGGGGTCCTTCAGCCACTCGGGCACCCCACCCAAATTTCGTTTCTTTCTTTCTTGGACggg                                                  >  2:1055607/1‑148 (MQ=2)                                                                                                gTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCt                                              <  2:592143/151‑1 (MQ=255)                                                                                                  aCTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGTTGGAACCCCCGCCACTTTGTCCTATACCA‑ACTTTTCAGGGGTGCTCCTTCAGCCCCTCGGGCACCCCACCCCATTTTCGTTCCTGTTTTTCTGGGACGGgcg                                                >  1:1180589/1‑147 (MQ=9)                                                                                                  aCTTTCGTACGAGCTCTTCTTTAAATATGGCGGTCAGGGGGGGTTTCACACCCCCGACTCATTTTCGTTGATAC‑ACTTTCCCCGCGTGTCGCTTCCGGCCCTCCGCAACCCCACCCCATTGTCCTTTCCGCCTTCCTGGAACgg                                                   >  1:107566/1‑144 (MQ=2)                                                                                                     ttCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAAt                                           <  2:610593/149‑1 (MQ=255)                                                                                                        gTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAgg                                      <  1:1188034/151‑1 (MQ=255)                                                                                                        gTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAgg                                      <  1:1354792/151‑1 (MQ=255)                                                                                                         tACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAACCCCCCATACGTTTCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCCCACCCAATTTTCGTTCCTGTCTTTTTGGGACGGGCGCCCATTTTggg                                     >  2:121224/1‑151 (MQ=14)                                                                                                           cGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGAACCCCCGATACGTTGCCGTATAAAC‑ACCTTCCAGGCGGGCTCCTTCAGCCACCCGGGCACCTCACCAAAATTTCGTTCCTGTCTTTCTGGGACGGGCGCCCATTTAtgg                                     >  2:665768/1‑149 (MQ=14)                                                                                                            gAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGAAACCCCCATACGTTTCCGTATACAC‑ACCTTCCAGGCGGGCTCCTTCCGCCCCTCGGACACCCCCCCCAAATGTCGTTTCTGTCTTTCTGGAACGGGGGCCAATTTTgggga                                   >  2:1302354/1‑148 (MQ=14)                                                                                                                               gCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTcaac                >  2:436969/1‑150 (MQ=255)                                                                                                                                    gatggggggATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACtt          >  2:157727/4‑151 (MQ=255)                                                                                                                                    gAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACt           <  1:137890/150‑1 (MQ=255)                                                                                                                                     aGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACttt         >  2:784182/1‑151 (MQ=255)                                                                                                                                      gggggggATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACtttt        <  2:426693/151‑1 (MQ=255)                                                                                                                                      gggggggATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGGGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCGGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACtttt        <  1:26505/151‑1 (MQ=255)                                                                                                                                         ggggATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGa     <  2:971594/151‑1 (MQ=255)                                                                                                                                            gATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGaaaa  <  2:1255535/151‑1 (MQ=255)                                                                                                                                             |                                                                                                                                                       CGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC‑ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAA  >  NC_000913/1097441‑1097730

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑