Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,163,377	0	G	T	43.9%	65.3 / 24.6	43	E40* (GAA→TAA)	thiK	thiamine kinase
Reads supporting (aligned to +/- strand):  ref base G (2/21);  new base T (18/0);  total (22/21)
Fisher's exact test for biased strand distribution p-value = 9.40e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATGGTAGTCG  >  NC_000913/1163232‑1163527                                                                                                                                                     |                                                                                                                                                         aCGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACAt                                                                                                                                                     <  1:724064/151‑1 (MQ=255)     gCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAgg                                                                                                                                                 <  1:908330/151‑1 (MQ=255)            tATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GG‑TTTTTTCTTTAACATCAagg                                                                                                                                                >  1:730070/1‑145 (MQ=255)                 ggTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GT‑TTTTTTTTTTAAAATCAGGGCCAG‑ccgttt                                                                                                                                     >  2:1011434/1‑145 (MQ=255)                              tGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GG‑TTTTTTTTTTAAAAACAAGGCCAG‑CGGTTTTTTTTGGGGCAggc                                                                                                                       >  1:882426/1‑149 (MQ=255)                                 cGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCCTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCa                                                                                                                    <  2:73887/151‑1 (MQ=255)                                  gTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GG‑TTTTTCTTTTTACATCACGGGCCG‑CGGTTTTTTGTGCGTCAGCCGccc                                                                                                                   >  1:42470/1‑149 (MQ=255)                                    ttCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACg                                                                                                                  <  2:977246/150‑1 (MQ=255)                                      cGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GG‑TTTTTTTTTTAACAACCAGGCCCG‑CGGTTTTTTTTGCGGCCGCCGCCCGaac                                                                                                               >  2:915740/1‑149 (MQ=255)                                           caATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGAt                                                                                                          <  1:450462/151‑1 (MQ=255)                                           caATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATAAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGAt                                                                                                          <  1:500134/151‑1 (MQ=255)                                            aataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GG‑TTTTTCATTTAACAACAAGGCCAG‑CGGTTTTTTTTGGGTCCGCCCCCCCATcc                                                                                                              >  1:676386/1‑146 (MQ=255)                                                       cACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GG‑TTTTTTTTTTAAAAACAGGGGCAGCCGTTTTGTTTTG‑GGCAGCCGCCCGGTCCTTGTGCGCCGCCGTcc                                                                                              >  1:487850/1‑151 (MQ=255)                                                              gacgaATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GG‑TTTTTTCTTTTACAACAGGGGCCA‑CGGTTTTTTTTGGGGCAGCCGCACAGGCCTGCTGggccgccggcc                                                                                              >  2:444110/1‑139 (MQ=255)                                                                 gaATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGAGGT‑TTTTTCTTTCAA‑ATCCAAGGCAG‑CGCTTTTTTTTGTGGTCGGCGCCCGCTCCTGGTGCGCCCCAGGCCGCGG‑Tc                                                                                       >  2:153505/1‑147 (MQ=255)                                                                   aTTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GG‑TTTTTCCTTTTAAATCAAGGCCAG‑CGGTTTTTTTTGGGGCCGCCGCCCCATCCCCATTCGCCCCCGTcccccgtttt                                                                                      >  1:385625/1‑139 (MQ=255)                                                                     tGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GG‑TTTTTTTTTTTAAATCAAGGGCAG‑CGGTTTTTTTTTGGTTCGCCCCCCGATCCTGATGCGCCGCCGGCCGCGG‑TCtt                                                                                     >  2:870806/1‑145 (MQ=255)                                                                      gCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCa                                                                               <  2:577175/150‑1 (MQ=255)                                                                           cgcgCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATc                                                                          <  1:497180/150‑1 (MQ=255)                                                                           cgcgCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATCg                                                                         <  2:698768/151‑1 (MQ=255)                                                                           cgcgCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATCg                                                                         <  2:179840/151‑1 (MQ=255)                                                                            gcgcTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATCgg                                                                        <  1:172347/151‑1 (MQ=255)                                                                             cgcTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GG‑TTTTTCCTTTTAAATCAAGGCCAG‑CGGTTTTTTTTGGGTCAGCCGCCCGAACCTGATGCGCCCCAGTCCCCGG‑TCTTTTGCCAGCATCggg                                                                       >  2:307140/1‑151 (MQ=255)                                                                              gcTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GG‑TTTTTCTTTTTAAATCAAGGGCAG‑CGGTTTGTTTTGGGTCAGGCGCACGGTCCCGATGCGCCCCCGAGCGCGTGTCTTG‑GCCCGGATCggg                                                                       >  2:308516/1‑150 (MQ=255)                                                                                  tttCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGG‑GT‑TTTTTTTTTTAAAACCA‑GGCCCG‑CGCTTTTTTTTGTGTCAGCCCCACGAACCTGGTGCGCCCCCCGCCCCGG‑TCTTTCGCCCGGATCGGGGtttt                                                                  >  1:687449/1‑150 (MQ=255)                                                                                     cccGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTTTCCTTTAACATCAGGGCCAG‑CGGTTTTTTGTTGGGCAGCCGCCCGATCCTGATGCGCCGCAGGCCGCGG‑TCTTGCGCCCGTATCGGGCttttt                                                                 >  2:64353/1‑147 (MQ=255)                                                                                        gCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGAGGT‑ATTTTCTTTTACAAAAAGGACCGG‑GGTTTT‑TTTTGGGGCACCCGCACCGTCCTGTTGCGCCGCAGGCGCCGG‑TGTTCTGCCCGTATCGGGGttt                                                                   >  2:479311/1‑144 (MQ=255)                                                                                          aGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GT‑TTTTTCATTTGACAACACGGGCCG‑CGCTTTTTTTTGCGGCAGCCGCACCGTCCCGATTCGCCGCAATCCGCGG‑TCTTTCGGCCGTATCCGGCttttttaaaa                                                            >  1:768495/1‑142 (MQ=255)                                                                                             atcatcCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATCGGGCTTTATCACAACTAc                                                        <  1:343504/150‑1 (MQ=255)                                                                                              tcatcCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTGTTTTTCTTTCTGAAT‑TTGGCCAG‑CGTTTTTTTTTTGGTCAGCGCCCCGGTCCTGCTGCTGCCCCGTCCGCCG‑TCTTGCGCCCGTATCGGGGTTTTTTTCAACTa                                                         >  2:420510/1‑148 (MQ=255)                                                                                               catcCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATCGGGCTTTATCACAACTACCCg                                                     <  1:936172/151‑1 (MQ=255)                                                                                                  cccGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATCGGGCTTTATCACAACTACCCgcat                                                  <  2:730060/151‑1 (MQ=255)                                                                                                        acgacgTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTg                                            <  1:679963/151‑1 (MQ=255)                                                                                                           acgTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCAc                                         <  2:882414/151‑1 (MQ=255)                                                                                                             gTTTAATAGTGGGCTTAGTGGCGGGGG‑GT‑TTTTTCTTTTAA‑ATTAAAACCCG‑CGTTTTTTTTTGGGGCAGCCGCACGATCCTTATGGGCCCCAGCCCGCGG‑TTTTTCGCCCGGATCGGGCGTTTTTACAACTACCCCCATGCATTTCAcc                                        >  2:583199/1‑150 (MQ=255)                                                                                                             gTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCg                                       <  1:945800/151‑1 (MQ=255)                                                                                                                 aaTAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAg                                    <  1:668893/150‑1 (MQ=255)                                                                                                                   tAGTGGGCTTAGTGGC‑GGGA‑GG‑TTTCTTATTTAACATCAAGGCCAG‑CGTTTTTTTGTGGGGCAGCCCCCCGAACCTTATGCGCCCCCGTCCCCCC‑TCTTTCGCCCGCATCCGGCTTTTTTACAACTACCcgcacgcactttaccca                                      >  1:301294/1‑137 (MQ=255)                                                                                                                        ggCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCAttt                            <  2:595606/151‑1 (MQ=255)                                                                                                                        ggCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCAttt                            <  1:294959/151‑1 (MQ=255)                                                                                                                                 gC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCg                   <  2:972320/151‑1 (MQ=255)                                                                                                                                         gT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTg             >  2:451476/1‑151 (MQ=255)                                                                                                                                                  aTTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATgg        >  2:195823/1‑148 (MQ=255)                                                                                                                                                     gAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATGGTAGTCg  >  1:186470/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                         ACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GT‑TTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGT‑TCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATGGTAGTCG  >  NC_000913/1163232‑1163527

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: ‑