Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,163,371	0	C	T	39.0%	57.7 / 19.5	41	L38F (CTC→TTC)	thiK	thiamine kinase
Reads supporting (aligned to +/- strand):  ref base C (3/22);  new base T (16/0);  total (19/22)
Fisher's exact test for biased strand distribution p-value = 9.40e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTGGTGCAGACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGC‑GTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGAT  >  NC_000913/1163222‑1163519                                                                                                                                                         |                                                                                                                                                        gCTGGTGCAGACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTtct                                                                                                                                                        <  1:541418/151‑1 (MQ=255)       gCAGACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGa                                                                                                                                                  <  1:471077/151‑1 (MQ=255)       gCAGACGGGCGAAATTATCTGGTCAGGTAAAGCGGCCGTTGCGCAGCAATAAGCCCATCACTCGCGACGAATTGCTGTCGCGGTTTGTCCCGCAGGATCATCCCGTCACGACGTTTAATAGGGTGCTGAGTGGC‑GGG‑AG‑TTTTCTCATTGa                                                                                                                                                  <  1:382114/151‑1 (MQ=255)        cAGACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGaa                                                                                                                                                 <  1:351036/151‑1 (MQ=255)                   aaTTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCa                                                                                                                                    <  1:617829/151‑1 (MQ=255)                         cTGGTCAGGTAAAGGTGCCGTTTAGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGAAG‑TTTTTTTTTTGAAA‑AT‑‑AGGGCCAGCg                                                                                                                                 >  2:537663/1‑148 (MQ=255)                           ggTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTttg                                                                                                                            <  2:390763/151‑1 (MQ=255)                               aGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTtgttgt                                                                                                                        <  2:478275/151‑1 (MQ=255)                                 gTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGc                                                                                                                      <  2:373136/151‑1 (MQ=255)                                   aaaGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑GTTTTTTTTTTTAA‑ATA‑AAGGCCAGCGGTTttttgtttg                                                                                                                     >  2:377313/1‑147 (MQ=255)                                       gTGCCGTTTCGCAGCACTAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCTCAGTATCATCCCGTCCCGACGTTTAAAAGTGGGCTGAGTGGC‑GGG‑AG‑TGTTCTCACTGAAC‑ATC‑AGGGCCAGAGTTTTGTGGGGCGTCAGc                                                                                                                <  1:25622/151‑1 (MQ=255)                                         gCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCGTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGcc                                                                                                               <  1:16938/150‑1 (MQ=255)                                               tCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑GG‑GTTTTTTATTTGAA‑AAC‑AGAGCCAGCGTTTTTTTGTGGGtgtgcc                                                                                                               >  2:137690/1‑139 (MQ=255)                                               tCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑GTTTTTCTTTTTAA‑AAA‑AGGGCCAGCGGTTTTTTGTGGGGCAGCCGCAc                                                                                                           >  2:462462/1‑148 (MQ=255)                                                cGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTGTCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGCCGCGCGAt                                                                                                        <  1:389492/150‑1 (MQ=255)                                                                 cACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑GG‑GTTTTTCCTTTTCC‑ATT‑AAGGGCAACGGTTTTTTGTGCGTGCGCCGCCCGacac                                                                                                      >  1:203453/1‑132 (MQ=255)                                                                                       cgcTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑GG‑GGTTTTTTTTTGAC‑AAC‑AAGGACAACGCTTTTTTTTGCGTGCGCCCCACGACCCTGATGCGCCGCCGACCGC‑GGTCTTTCGCCCGtctagg                                                                >  1:477591/1‑145 (MQ=255)                                                                                           ttttCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑GG‑GTTTTTTATTTAAA‑AAA‑AAGGCCCGCGGTTTTTTTTGTGGCCGCCGCCCGATCCCGATGCGCCGCCGTCCGC‑GGTCTTTTGCCCGGATCGGGGttt                                                           >  2:568875/1‑151 (MQ=255)                                                                                             ttCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑GG‑GTTTTTTATTTAACAAAC‑AGGGCC‑GCGGTTTTTTGTGGGGCAGCCGCACGAACCCGATGCGCCGCCGTCCCCGGTTCTT‑CGCCAGCATCGGGGttttt                                                         >  2:98803/1‑149 (MQ=255)                                                                                                ccGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGG‑GG‑TTTTTTCTTTGACC‑ACA‑AGGGCC‑GCGGTTTTTTTTGGGGTCGCCCCACGAACCCTATGCGCCGCCGGCCGC‑GGTTTTTCCCCCGTATTggggcttt                                                          >  2:116205/1‑142 (MQ=255)                                                                                                 cGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGC‑GTTCTTGCGCCAGTATCGGGCTTTATcaca                                                     <  2:595116/151‑1 (MQ=255)                                                                                                 cGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑GTTTTTCATTTTAA‑AAC‑AAGGCCCGCGGTTTTTTGTGGGTCAGCCGCCCGATACTGGTGCGCCGCAGGCCGC‑GTTCTTTCGCCCGTATCGGGGTTTTTccc                                                      >  2:200143/1‑148 (MQ=255)                                                                                                  gCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGC‑GTTCTTGCGCCAGTATCGGGCTTTATCACaa                                                    <  2:593689/151‑1 (MQ=255)                                                                                                     gTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGC‑GTTCTTGCGCCAGTATCGGGCTTTATCACAACTa                                                 <  2:252426/151‑1 (MQ=255)                                                                                                           tcCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑GG‑GTTTTTCATTTAAC‑ATC‑AAGGCCCGCGTTTTGTTTTGGGTCAGCCGCCCGAACCTGGTGCGCCCCCGGCCCC‑GGTCTTTCGCCCGGATCGGGGTTTTTTACAACCAccccc                                            >  2:109288/1‑148 (MQ=255)                                                                                                           tcCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑GG‑GTTTTTCATTTAAA‑ATC‑AGGGCCAGCGGTTTTTTTTGGGGCAGCCGCCCGAACCTGGTTCGCCGCAGGCCGC‑GGTCTTTCCCCCGGATCGGGCTTTTTTACaaacaaccccc                                           >  2:188519/1‑142 (MQ=255)                                                                                                              cGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑GGTTTTTTTCCTTTAA‑‑ATCAATGCCCCGCCTTTT‑TTGTGGGGCAGGCGCACCATCCTGATGCGCCCCCGGCCGC‑CGTCTTTCGCCAGGCACGGGCCTTTTCCCAACCAcccccccgc                                        >  1:8167/1‑145 (MQ=255)                                                                                                                 cACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑GG‑GTTTTTCTTTTAAA‑ATC‑AAGGCCCGCGGTTTTTTTTGCGTCAGCCCCCCCATCCTGATGCGCCCCAGGCCCC‑GCTCTTTTGCCCGGATCGGGCGTTTTCACAAATAACCCCCTGCAtt                                     >  2:449706/1‑151 (MQ=255)                                                                                                                 cACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGC‑GTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCgcatgcat                                      <  1:580631/150‑1 (MQ=255)                                                                                                                  ccgacgTTTAATAGTGGGCTTAGTGGC‑GGG‑GG‑TTTTTTCTTTTAAC‑AAC‑AAAGCAAGCGGTGTTTTGTGGGGCAGGCGCCCCATCCCGCATAGCCGCCCGCCGC‑GTTTTTTCGCCCGCATCGGGCGTTTTtacacaatccccccgac                                        >  1:621713/2‑134 (MQ=255)                                                                                                                  acgacgTTTAATAGTGGGCTTAGTGGC‑GGG‑GG‑GTTTTTCCTTTAAA‑ATA‑AAGGGCCGCGGTTTTTTTTTCGGCAGCCGCCCCCACCTGATGCCCCGCCGTCCGC‑GGTCTTGCCCCCGGATCGGGGGTTTTTACAACCACCCCCCTGCCtt                                     >  2:555201/1‑150 (MQ=255)                                                                                                                   cgacgTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGC‑GTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTg                                    <  1:214135/150‑1 (MQ=255)                                                                                                                    gacgTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGC‑GTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGc                                   <  2:182474/150‑1 (MQ=255)                                                                                                                    gacgTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGC‑GTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCa                                  <  1:479308/151‑1 (MQ=255)                                                                                                                     acgTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGC‑GTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCAc                                 <  1:515203/151‑1 (MQ=255)                                                                                                                     acgTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGC‑GTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCAc                                 <  1:595642/151‑1 (MQ=255)                                                                                                                       gTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGC‑GTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCg                               <  2:287982/151‑1 (MQ=255)                                                                                                                               gttggCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCGGATGCGCCGCAGTCCGC‑GTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGcg                       <  1:548097/148‑2 (MQ=255)                                                                                                                               gTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGC‑GTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCa                       <  1:411697/151‑1 (MQ=255)                                                                                                                                         tGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGC‑GTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATAtctc             >  2:474310/1‑151 (MQ=255)                                                                                                                                                  aG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGC‑GTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACt      >  1:619939/1‑151 (MQ=255)                                                                                                                                                       ttCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGC‑GTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGAt  >  1:585358/1‑151 (MQ=255)                                                                                                                                                         |                                                                                                                                                        GCTGGTGCAGACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGG‑AG‑TTTTCTCATTGAAC‑ATC‑AGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGC‑GTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGAT  >  NC_000913/1163222‑1163519

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑