Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,097,581	0	A	G	44.0%	71.1 / 15.6	50	noncoding (72/88 nt)	serX	tRNA‑Ser
Reads supporting (aligned to +/- strand):  ref base A (6/22);  new base G (22/0);  total (28/22)
Fisher's exact test for biased strand distribution p-value = 5.24e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAA  >  NC_000913/1097436‑1097730                                                                                                                                                  |                                                                                                                                                        cACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑Ga                                                                                                                                                   <  1:323674/151‑1 (MQ=31)       gTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAAccccc                                                                                                                                             <  1:779822/151‑1 (MQ=35)        ttCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAAccccc                                                                                                                                             <  2:58555/150‑1 (MQ=35)                           gCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTC‑GAACCCCCCCTACGTTGCCGTATaca                                                                                                                           >  1:828814/1‑149 (MQ=255)                                cGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTc                                                                                                                    <  1:158324/151‑1 (MQ=255)                                   cAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTT‑GAACCCCCCATACGTTTCCGTATACACACttt                                                                                                                     >  2:197657/1‑147 (MQ=255)                                     gTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTC‑GAACCCCCCCTACGCTTCCCTATTCACACCTTTCAgg                                                                                                                >  2:627525/1‑150 (MQ=11)                                        gTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTg                                                                                                            <  2:430149/151‑1 (MQ=255)                                               cccGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTC‑GAACCCCCCATAAGTTGCCGGATAAACACTTTCCAGGGGCGCTccct                                                                                                      >  1:592285/1‑148 (MQ=17)                                                   gTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGcc                                                                                                 <  1:621127/151‑1 (MQ=255)                                                     cGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCAc                                                                                               <  2:532610/151‑1 (MQ=255)                                                       gggCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTC‑GAACCCCCCATACGGTTCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCAccc                                                                                             >  1:461516/1‑149 (MQ=255)                                                         gCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCgg                                                                                           <  1:339567/151‑1 (MQ=255)                                                         gCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGCGAGGGGGGGGTTC‑AAACCCCCCCAACGTTGCCGTATTAACCCTTTTCAGGGGTGGCCCTTCAGcccccccg                                                                                           >  1:674812/1‑145 (MQ=14)                                                            tttcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGac                                                                                         <  2:339194/148‑1 (MQ=255)                                                                    ccccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTT‑GAAACCCCCATACGTTGCCGTATACACACTTTTCCGGCGGGCTCCTTCCGCCACTCCGACAccccccc                                                                                 >  1:760549/1‑145 (MQ=17)                                                                      ccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCA‑CCaaa                                                                             <  1:608348/151‑1 (MQ=255)                                                                       cGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAAACCCCCATACGTTGCCGTATAAACACTTTCCAGGCGGGCTCCTTCAGCCACCCCGACAACCCA‑CCaaa                                                                             >  2:399112/1‑150 (MQ=14)                                                                        ggTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCA‑CCAAAtt                                                                           <  1:799977/151‑1 (MQ=255)                                                                         gtgtgtGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACTCACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACTCCTCA‑CCAAAt                                                                            <  2:20046/149‑1 (MQ=255)                                                                            tgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTTTACACACTTTCCCCGCGTGCTCCTTCAGCCACCCGGGCACCCCC‑CCaaaattt                                                                         >  1:554458/1‑145 (MQ=14)                                                                              tgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTT‑GGACCCCCGATACGTTGCCGTATACACACTTTTCCGGCGGGCTCCTTCCGCCACTCCGACACCTCA‑CCCAATTGTCGtt                                                                     >  1:61355/1‑151 (MQ=14)                                                                                   tataCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTT‑GAAACCCCCATACGTTGCCGTATAAACACTTTTCAGGCGGGGCCCTTCAGCCACTCCGAAACACCACCCAAAtttcttttc                                                                    >  2:685381/1‑141 (MQ=11)                                                                                     taCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTC‑GAACCCCCCATACGTTTCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACCCGGACACCCCA‑CCAAAATTTCGTTcc                                                                   >  1:299244/1‑146 (MQ=14)                                                                                       cGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTC‑GAAACCCCCCTACGTTTTCGGATAAACACTTTTCCGGCGGGCTCCTTTAGCCCCCCCGGCACCCCC‑CCCAAATTTTGTTCCCGTCtt                                                             >  1:103109/1‑150 (MQ=2)                                                                                        gAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGc                                                           <  2:816679/151‑1 (MQ=255)                                                                                        gAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGAGAGGGGGGGGTTT‑GGACCCCCCATACGTTTTCGTATACACACATTCCAGGGGGGGCCCTTCAGCCACCCGGGCACCCCA‑CCCAATTATTGTTCCTGTCttt                                                            >  2:170368/1‑149 (MQ=14)                                                                                         aaaaaaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGAGAGGGGGGGGTTC‑GAACCCCCCGCAAGTTTCCGTATACACCCTTTTCAGGGGGGCTCCTTCAGCCACCCCGACCCCTCA‑CCAAAATTTTGTTCCTGtttt                                                             >  2:579210/1‑148 (MQ=11)                                                                                           aaaaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGGGAGGGGGGGGTTC‑GAACCCCCCATACGTTGCCGTATACACACCTTCCACGCGGGCTCCTTCAGCCACTCGGACACCTCC‑CCCAATTTTCGTTCCTGTCTTTCTgg                                                        >  1:807278/1‑151 (MQ=14)                                                                                                 gCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTC‑GAACCCCCCCTACGTTTCCCTATACACACCTTCCACGCGGGCTCCCTCAGCCACCCCGACACCCCC‑CCCAAATTTCGTTCCTGTCTTTCTggga                                                      >  1:741577/1‑145 (MQ=14)                                                                                                    cGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTT‑TGACCCCCGACACCTTTCCGTATAAACAACTTTCAGGGGTGCTCCTTCAGCCCCTCGGGCACCCCA‑CCCAATTTTCGTTCCTGTCTTGCTGGGACGGgcg                                                >  2:107043/1‑150 (MQ=17)                                                                                                       aCTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCTGAACCCCC‑ATACGTTTGCGTATACACACTTTTCCGGCGTGCTCCTTCAGCCACCCGGGCACCCCA‑CCCAAATTTCGTTCCTGTCTTGCTGGAACGGgcg                                                >  2:293198/1‑147 (MQ=17)                                                                                                        cTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTT‑GGACCCCCCATACGTTGTCCTATACACACTTTTCAGGCGTGCGCCTTCAGCCACTCGGACACCTCC‑CCAAATTTTTGTTCCTGTCTTTCTGGGAAGGgggc                                               >  2:210947/1‑147 (MQ=11)                                                                                                          ttCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAAtt                                          <  2:104196/150‑1 (MQ=255)                                                                                                             gTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTC‑GAACCCCCCATACGTTGCCGTATACACACTTTTCAGGCGGGCTCCTTCAGCCACCCGGACACCTCA‑CCAAATTTTCGTTTCTGTCTTTCTGGGAAGGGCGCTAAttt                                         >  1:321224/1‑148 (MQ=14)                                                                                                             gTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAgg                                      <  2:41178/151‑1 (MQ=255)                                                                                                               aCGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTT‑GAAACCCCCATACGGTGCCGGATAAACACCTTTCAGGCGTGGCCCTTCAGCCCCCCCGACACCCCA‑CCCAATTTTTGTTCCTGTCTTTCTGGGACGGGCGCCAATTTAggg                                     >  1:343189/1‑150 (MQ=12)                                                                                                               aCGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAggg                                     <  2:553242/150‑1 (MQ=255)                                                                                                                cGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTC‑GAACCCCCCCTACGTTTCCGTATAAACACTTTCCAGGCGTGCTCCTTCAGCCACCCGGACACCCCA‑CCAAATTTTCGTTCATGTCTTGCTGGGACGGGGGCTCATTTAggg                                     >  1:246729/1‑149 (MQ=17)                                                                                                                         cttTAAATATGGCGGTGAGGGGGGGGGTT‑GAACCCCCGGTAAGTTGCCGTATAAAAAATTTTCAGGGGGGGTCCTTCAGACACCCGGGGACCCCA‑CCAAAATGTCGTTCCTGTTTTTCTGGGAAAGGCGCCAATTTAAGGAAATAACGAcc                          >  2:60908/1‑151 (MQ=9)                                                                                                                         cttTAAATATGGCGGTGAGGGGGGGAATC‑GAACCCCCCGTAACTTGCCGTCTAAACACATTTCAGGGGGGGTCCTTCAGCCACTCGCACACCCCA‑CCAAAATTTCGTTCCCGTCTTTTTGGAACGGGGGCCAAATTTTGGAAAAAATGAc                           >  2:841686/1‑150 (MQ=9)                                                                                                                            tAAATATGGCGGTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTg                        <  1:380166/150‑1 (MQ=255)                                                                                                                             aaaTATGGCGGTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGa                       <  1:412173/150‑1 (MQ=255)                                                                                                                                       gTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAAc            <  2:327698/151‑1 (MQ=255)                                                                                                                                         gAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGTGTGCTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACtt          >  1:213395/1‑151 (MQ=255)                                                                                                                                         gAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACt           <  2:65460/150‑1 (MQ=255)                                                                                                                                            ggggggATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACttttt       >  1:265253/1‑151 (MQ=255)                                                                                                                                             gggggATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTg      >  1:172847/1‑151 (MQ=255)                                                                                                                                              ggggATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGa     <  2:754319/151‑1 (MQ=255)                                                                                                                                                 gATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGaaaa  <  1:446147/151‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                        CACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTC‑GAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAA  >  NC_000913/1097436‑1097730

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑