Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,222,596	0	G	A	47.7%	25.8 / 30.5	44	F13F (TTC→TTT)	ymgD	uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base G (20/3);  new base A (0/21);  total (20/24)
Fisher's exact test for biased strand distribution p-value = 1.02e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTACCGCAACAATTTCTGCAACCTGTGCGCTGTCAGTTTTTGCCATT‑TCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGG‑CAAACCGTTTTT‑AATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTCAGAACGCCA  >  NC_000913/1222465‑1222734                                                                                                                                       |                                                                                                                                           attaccGCAACAATTTCTGCAACCTGTGAGCTGTCAGTTTTTGCCATT‑TCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGG‑CAAACCGTTTTT‑AATATTGTAGTCCTGCGCCCAGGTCATTGGTTCGAAAGCAAACTGGCCCGCCa                                                                                                                         <  1:572201/151‑1 (MQ=255)     ccGCAACATTTTCTCCACCCTGTGCGCTGTCATTTTTTGCATTT‑TCGTTGTTTTCTGCGCAAGAAATATAGTTTTCGGACGG‑CAAACCTTTTTT‑AATTTTGTAGTCCTGCGCCCGGGTCATTGGGGCGAAAACAAACAGGCCCGCCAGTaa                                                                                                                     <  1:502030/151‑1 (MQ=255)      cGCAACAATTTCTGCAACCTGTGCGCTGTCAGTTTTTGCCATT‑TCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGG‑CAAACCGTTTTT‑AATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTaa                                                                                                                     >  1:748909/1‑150 (MQ=255)        caacaaTTTCTGCAACCTGTGCGCTGTCAGTTTTTGCCATT‑TCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGG‑CAAACCGTTTTT‑AATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGc                                                                                                                  >  2:991901/1‑151 (MQ=255)            attttCTGCACCCTGTGCTCTTTCTGTTTTTGCCATT‑TCGTGGGTTTCTGCAAAATTAATATAGGTTTCGGACGG‑CAACCCTTTTTT‑AATATTGTGGTCCTGCCCCAAGGTCTTTGGTGCAAAAACAACCAGGCCCGCCAGTAAAGCaa                                                                                                                <  1:1031011/147‑1 (MQ=255)                       ccTGTGCGCTTTGA‑TTTTTTCCATTCTGGTGTGTTTCTGCGAAAAAAATAGAGGTTTCTGCCGA‑CAACCTTTTTTA‑AATTTTTTACCCTTCCGCCAATTTTTTTGGTCAAAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTtcat                                                                                                      <  1:415119/148‑1 (MQ=255)                            gcgtTGTCAGTTTTTGCCTTT‑TCGTTGGCTTCTGCGAAAGAAATATAGGTTTCTGACGG‑CAACCCTTTTTT‑AATATTGTAGCCCTGCCCCCAGGTCATGGGTGCAAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTcatcatcat                                                                                                <  2:14731/149‑1 (MQ=255)                                tGTCAGTTTTTGCCATT‑TCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGG‑CAAACCGTTTTT‑AATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCtt                                                                                           >  1:645407/1‑150 (MQ=255)                                  tCATTTTTTCCCTTT‑TCGTTGGTTTCGGCGAAAGTAATATAGTTTTCGGGCGG‑CAAACCTTTTTT‑AATATTGTAGTCCGGCGCCCATGTTTTTGGTGCAAAAACAAACGGCCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCtt                                                                                           <  1:502863/148‑1 (MQ=255)                                  tCAGTTTTTGCCTTT‑TCTTTGGTTTCTGCGAAAGTAATATAGGTTCCGGACGG‑AAACCCTTTTTT‑AATTTTGTGGTCCTGCCCCAAGTTCTTGGGTGCAAAAACAAACGGCCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCtt                                                                                           <  1:882926/148‑1 (MQ=255)                                     ttttttGCCTTT‑CCTTTGTTTTTTGCGAAAAAATTATAGTTTTCGGAGGG‑CAACCCTTTTTT‑AATTTTGTGGCCCTGCGCCAATTTCTTTGGGGAAAAAAAAACCAGCCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTAtt                                                                                        <  1:660505/147‑1 (MQ=255)                                      tttttGCCATT‑TCGTGGGTTTCTGCGAAAGTAATATAGGTTTCTGACGG‑CAAACTGTTTTT‑AATTTTGTAGTCCTCCGCCAAGGTTATTGGTGCAAAAAAAAACGGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCt                                                                                            <  2:816324/143‑1 (MQ=255)                                      ttttgctcttt‑tCTTTGGCTTCTCCGAAAGTAATAATGTTTTGTACCGG‑CAAACTTTTTTG‑AATATTTGGCTCCTGCCCCAAGTTTGTTGGGGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTtcatc                                                                                                     <  1:210026/125‑1 (MQ=255)                                       tcttGCCATT‑TCGTTGGCTTCTGCGCAAGTAATATAGGTTCCTGACGG‑CAAACCGATTTT‑AATATTGTAGTCCTACGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCAtt                                                                                   >  1:450499/3‑151 (MQ=255)                                         ttGCCTTT‑TCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGG‑CAAACCTTTTTT‑AATATTGTAGCCCTGCGCCCAGTTCTTTGGTGCAAAAAAAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCAttt                                                                                  <  2:581383/150‑1 (MQ=255)                                           tcctttttcttggtcTTCTGCGCAAGTAATATAGTTTTCT‑ACGGCCAAACCTTTTTT‑AATATTTTAGTCCTCCCCCCATGTTATTGGTCCAAAAACAAACTGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCAtttt                                                                                 <  1:256606/136‑1 (MQ=255)                                           gCCATT‑TCGTTGGCTTCTGCGCAATTAATATAGTTTTCTGACGG‑CAACCCTTTTTA‑AATTTGGTAGTCCTCCCCCAAGTTCATTGGTGAAAAAACAAACGGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCAtttt                                                                                 <  1:330865/149‑1 (MQ=255)                                            ccttt‑tCTTTGGCTTCTGCGCAACTAATATGGTTTTCTGACGG‑CACCCCTTTTTT‑AATATTGTAGTCCTGCCCCAAGGTCTTTGGTGCAAAAACAACCAGCCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTa                                                                                <  2:520690/146‑1 (MQ=255)                                             cATT‑TCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGG‑CAAACCGTTTTT‑AATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTAccc                                                                             >  1:57483/1‑151 (MQ=255)                                             cATT‑TCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGG‑CAAACCGTTTTT‑AATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTAccc                                                                             >  1:661562/1‑151 (MQ=255)                                               tt‑tCTTTGGTTTCTGCGCAAGTAATATGGGTTTCTGACGG‑CAACCCTTTTTT‑AATTTTGTAGTCCTGCCCCCAGTTCATTGGTGCAAAAACAAACAGCCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCa                                                                            <  2:391246/150‑1 (MQ=255)                                               tt‑tCTTTGGTTTCTGCGAAAGAAATATGGTTTTCGGACGC‑CAAACCGTTTTT‑AATATTGTAGCCCTGCCCCCAGGTTTTGGGTGCAAAAACAAACAGCCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTAccc                                                                             <  1:853398/149‑1 (MQ=255)                                                     ttGGTTTCTGCGAAAGTAATATAGTTTTCTGACGG‑CAAACCTTTTTA‑AATATTGTAGTCCTGCCCCCAGTTCATTGGTGCAAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAAtt                                                                       <  2:1023769/150‑1 (MQ=255)                                                          ttCTGCGCAAGTAATATAGGTTTCTGACGG‑CAAACCGTTTTT‑AATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGcacc                                                                  >  2:149403/1‑150 (MQ=255)                                                          ttCTGCGCAAGTAATATAGGTTTCTGACGG‑CAAACCGTTTTT‑AATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGcacc                                                                  >  2:460867/1‑150 (MQ=255)                                                                cgaaagaaatattgTTTTTGACGG‑CCAACCTTTTTTAAATTTTAAACTCTGGCGCCCGGTTCATTGGTCCAAAAACAAACAGCCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGcacca                                                                 <  1:227390/133‑1 (MQ=255)                                                                 cAAGTAATATAGGTTTCTGACGG‑CAAACCGTTTTT‑AATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTAc                                                          >  2:956416/1‑151 (MQ=255)                                                                  aagtaagtTGGGTTTCGGCCGG‑CAACCCGTTTTA‑AATTTTGTAGCCCGGCCCCCGGTTTATTGGGGCAAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCg                                                             <  2:198169/147‑1 (MQ=255)                                                                  aaGTAATAAAGGTTTCTGACGA‑AAACCCTTTTTT‑AATTTTGTAGCCCTGCCCCCGGTTCATGGGTGCAAAAAAAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGcaccac                                                                <  2:462107/144‑1 (MQ=255)                                                                  aaGAAATATAGGTTTCTGACGG‑CAACCCTTTTTT‑AATTTTGTAGCCCTGCCCCAAGGTCTTTGGTGCAAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTAcc                                                         <  2:352835/151‑1 (MQ=255)                                                                    gaaaTATAGGTTTCTGACGG‑CAAACCGTTTTT‑AATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCg                                                        >  1:830690/3‑150 (MQ=255)                                                                    gTAATATAGGTTTCTGACGG‑CAAACCGTTTTT‑AATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGc                                                       >  2:868996/1‑151 (MQ=255)                                                                              tttCTGACGG‑CAAACCGTTTTT‑AATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACgg                                              >  1:134003/1‑150 (MQ=255)                                                                                     cGG‑CAACCCTTTTTT‑AATTTTGTAGTCCGGCCCCAAGTTCTTTGGTGAAAAAACAAACGGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCttt                                       <  2:1027080/150‑1 (MQ=255)                                                                                       g‑CAAACCGTTTTT‑AATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAAt                                    >  1:472957/1‑151 (MQ=255)                                                                                              cGTTTTT‑AATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGcccc                              >  2:451263/1‑151 (MQ=255)                                                                                              cGTTTTT‑AATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGcccc                              >  2:929801/1‑151 (MQ=255)                                                                                               ttttta‑AATTTTGTAGCCCCGCCCCCGGTTTTTTGGTGAAAAAACAACCACCCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGcccc                              <  1:590744/149‑1 (MQ=255)                                                                                                ttttt‑AATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCtt                            >  1:1010554/1‑151 (MQ=255)                                                                                                                 ccTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGt            >  2:818251/1‑151 (MQ=255)                                                                                                                  cTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTc           >  2:384160/1‑151 (MQ=255)                                                                                                                     cgcCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTc           >  1:525546/1‑148 (MQ=255)                                                                                                                      gcCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTCAGa        >  2:867078/1‑150 (MQ=255)                                                                                                                           ggTTATGGGTGCAAAAACAAACGCGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTCAGAACGCCa  <  1:427021/151‑1 (MQ=255)                                                                                                                                       |                                                                                                                                           ATTACCGCAACAATTTCTGCAACCTGTGCGCTGTCAGTTTTTGCCATT‑TCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGG‑CAAACCGTTTTT‑AATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTCAGAACGCCA  >  NC_000913/1222465‑1222734

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑