Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,163,371	0	C	T	41.3%	56.8 / 30.7	46	L38F (CTC→TTC)	thiK	thiamine kinase
Reads supporting (aligned to +/- strand):  ref base C (3/24);  new base T (19/0);  total (22/24)
Fisher's exact test for biased strand distribution p-value = 3.71e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTGGTGCAGACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAT‑CGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATG  >  NC_000913/1163222‑1163520                                                                                                                                                        |                                                                                                                                                        gCTGGTGCAGACGGGCGAAATTATCTAGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCGTCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTtct                                                                                                                                                        <  2:776380/151‑1 (MQ=255)     gTGCAGACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCAtt                                                                                                                                                    <  1:72444/151‑1 (MQ=255)                  aaaTTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGcc                                                                                                                                       <  2:111923/151‑1 (MQ=255)                   aaTTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GGTTTTTCtttttaaaatcaggccc                                                                                                                                      >  1:1025714/1‑137 (MQ=255)                           ggTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GGTTTTTTATTTTAAAACATGGCCCG‑CGgttt                                                                                                                              >  2:211058/1‑150 (MQ=255)                               aGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTtgttgt                                                                                                                         <  1:330191/151‑1 (MQ=255)                                  tAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GGTTTTTTCTTTTACAAATGGGCCAG‑CGTtttttt                                                                                                                           >  1:1050260/1‑146 (MQ=255)                                   aaaGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGt                                                                                                                     <  2:1105985/151‑1 (MQ=255)                                      ggTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GGTTTTTCCTTTTAACTCAAGGCCCG‑CGgttt                                                                                                                              >  1:673048/1‑139 (MQ=255)                                                      aataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GGTTTTTCTTTTTAAATCAAGGCCCG‑CCGCTTGTTGTGCGTCCGGCCCCCGATCCTGAt                                                                                                   >  2:705445/1‑150 (MQ=255)                                                       ataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATgc                                                                                                 <  2:915003/151‑1 (MQ=255)                                                          atCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GTGTTTTTATTTTAAATAAAGGCCCG‑CGGTTTGTTGTGGGGGCGCCGCGCGCTCCCGGTgcggc                                                                                              >  1:253760/1‑149 (MQ=255)                                                            cccATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GGTTTCTCTTTTTACATCACGGCCAGCCGTTTTTTTTTG‑GGCAGCCGCCCCACCCTGATGcgcc                                                                                              >  1:1149351/1‑149 (MQ=255)                                                            cccATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGcgccg                                                                                             <  2:685454/150‑1 (MQ=255)                                                                 cACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GGTTTTTCTTTTTAAAACAAGGCCCG‑CGGTTTGTTGTGCGGCAGCCGCGCCAGCCTGTGGCGCCGCCGTcc                                                                                       >  1:243012/1‑151 (MQ=255)                                                                 cACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTcc                                                                                       <  2:1047937/151‑1 (MQ=255)                                                                  aCGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCcg                                                                                      <  2:338021/151‑1 (MQ=255)                                                                      gcgACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GGTTTTTCATTTAAAAACAAGGGCCG‑CGGTTTTTTTTGGGTCCGCCCCCCGAAACTGATGcgcccccggcc                                                                                       >  2:589702/1‑139 (MQ=255)                                                                        gacgaATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCt                                                                                <  2:1892/151‑1 (MQ=255)                                                                         acgaATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCtt                                                                               <  2:553250/151‑1 (MQ=255)                                                                           gaATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GGTTTTTTCTTTTTCAATAAGGCCAG‑CGTTTTTTTTTGAGGGAGGCGCCCCATCCCTATgcgcaggcgtcagccgt                                                                                  >  2:284504/1‑133 (MQ=255)                                                                            aaTTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTgcg                                                                            <  1:1057551/151‑1 (MQ=255)                                                                             aTTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTgcgc                                                                           <  2:535486/151‑1 (MQ=255)                                                                                gCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGTTTAGTGGC‑GGGG‑GGTTTTTTATTTTAAAACAAGGACAG‑AGGTTTTTTGTGCGTCGGCCGCCCGAACCTGGTTCGGCGCCGTCCGCGGTCTTtcg                                                                            >  1:1037496/1‑147 (MQ=255)                                                                                gCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGAGGGTTTTTCTTTTAA‑ACCACTGCCAG‑CGGTTTTTTTTGTGGCCGCCGCCCGCTCCTGATGGGCCCCCGGCCGCCGTCTTTCGccc                                                                         >  1:647779/1‑149 (MQ=255)                                                                                     cgcgCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GGTTTTTTTTTTAAAAAAAGGGGCCG‑CGGTTTTTTTTGGGGCCGGCCCACGACCCCGATGCGCCCCAGGCCCCGTTCtt                                                                               >  2:1051919/1‑139 (MQ=255)                                                                                     cgcgCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAT‑c                                                                   <  2:25699/150‑1 (MQ=255)                                                                                       cgcTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGC‑GTTTTTTTCTTTTAAACCAAGGCCAG‑CGTTTTGTTTTGCGTCAGCCCCACGAACCCGCTGGGCCGCCGTCCCCGGTCTTGCTcccatattcg                                                                  >  2:1128027/1‑142 (MQ=255)                                                                                             ttCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GGGTTTTTATTTTAAAACAATGCCCA‑CGTTTTTTTTTGTGGCATGCGCACCAGCCTCATTCGCCGCCGCCCGCGTTCTTTCGCCCCTAT‑CGGGGTTTAt                                                          >  2:1021189/1‑151 (MQ=255)                                                                                               cccGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAT‑CGGGCTTTATc                                                         <  1:663164/150‑1 (MQ=255)                                                                                                 cGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAT‑CGGGCTTTATcaca                                                      <  2:221806/151‑1 (MQ=255)                                                                                                    aGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAT‑CGGGCTTTATCACAACt                                                   <  1:520171/151‑1 (MQ=255)                                                                                                       atcatcCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAT‑CGGGCTTTATCACAACTAc                                                 <  2:596487/150‑1 (MQ=255)                                                                                                         catcCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGG‑GTTTTTTCTTTAAAATTAAGGCCCAC‑GGTTTTTTTTTGGGGC‑GACCCCCGAACCCGGTGCGCCGCCGGCCCCGCTCTTTCGGCCGTAA‑CGGGGTTTTTTACCACTAcccc                                              >  1:1137811/1‑150 (MQ=255)                                                                                                         catcCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GGTTTTTCCTTTAAAATCAAGGGCAG‑CGGTTTTTTTTGTGGCAGCCGCCCGATCCTGATTCGCCCCCCGCCCCGGTCTTTCGCCCCTATCCGGGCTTT‑TTACAACTAccc                                               >  2:308680/1‑150 (MQ=255)                                                                                                         catcCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GGTTTTTCCTTTAAAAACAAGGCCCG‑CGTTTTGTTTTGGGTCAGCCGCCCGGACCTGAATCGCCGCCGTCCGCCGTCTTTCGCCCGCAT‑TGGGCCTTATTACCACCAcccc                                              >  2:349362/1‑150 (MQ=255)                                                                                                             ccGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GTTTTCTTCTTGAACATCAAGGGCAG‑CGGTTTTTTTTGTGGGTGCCGCCCGAACCTGATGCGGCGCCGGCCGCGCTCTTTTGCCCGGAT‑CGGGCTTTTTTACAAATAcccccc                                            >  1:17550/1‑146 (MQ=255)                                                                                                               gTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAT‑CGGGCTTTATCACAACTACCCgcatgca                                        <  2:532420/151‑1 (MQ=255)                                                                                                                 cACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GGTTTTTCCTTTAAAATCAAGGGCAA‑CGGTTTTTTGTGCGGTAACCGCACCGACCTGCTGCGCCGCCGTCCCCGGTCTTTCGCCACGAT‑CGGGGCTTTTCACAAATAccccc                                             >  2:999619/1‑142 (MQ=255)                                                                                                                     acgTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAT‑CGGGCTTTATCACAACTACCCGCATGCATTGCAc                                  <  1:287320/151‑1 (MQ=255)                                                                                                                      cgTTTAATAGTGGGCTTAGTGGC‑GGGA‑GGTTTTTTATTTTAAAACAAGGCCAG‑CGGTTTTTTGTGGGTCAGCCGCACGATCCCGATGCGCCGCAGTCCGCGGTCTTTCGCCCGGAT‑CGGGGCTTTTTACAACTACCCCCCTGCCTTTCAcc                                 >  2:7537/1‑151 (MQ=255)                                                                                                                          tAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAT‑CGGGCTTTATCACAACTACCCGCATGCATTGCACCGaa                              <  2:391564/150‑1 (MQ=255)                                                                                                                            aTAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAT‑CGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGcc                           <  1:527529/151‑1 (MQ=255)                                                                                                                                       aGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAT‑CGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTatat                 <  1:643766/150‑1 (MQ=255)                                                                                                                                        gTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAT‑CGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATAtct               <  1:575859/151‑1 (MQ=255)                                                                                                                                          ggC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAT‑C‑GGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTcc             >  1:296729/1‑150 (MQ=255)                                                                                                                                               ggA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAT‑CGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGa         <  2:363419/151‑1 (MQ=255)                                                                                                                                                       tctcATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAT‑CGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGAt   <  2:72256/150‑1 (MQ=255)                                                                                                                                                       tctcATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAT‑CGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATg  >  2:18668/1‑151 (MQ=255)                                                                                                                                                        |                                                                                                                                                        GCTGGTGCAGACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACATCAGGGCCAG‑CGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAT‑CGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATG  >  NC_000913/1163222‑1163520

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: ‑