Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,764,774	0	G	A	48.8%	45.6 / 18.6	41	intergenic (‑388/+160)	sufA/ydiH	Fe‑S cluster assembly protein/uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base G (19/2);  new base A (0/20);  total (19/22)
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

ATGACTATTTAAGAGATAGGTAAAAAAGTGCAGCGTTCAGAAATAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCC‑CATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCGATTTGGCGAACTTGCGGCATT  >  NC_000913/1764628‑1764924                                                                                                                                                     |                                                                                                                                                       aTGACTATTTAAGAGATAGGTAAAAAAGTGCAGCGTTCAGAAATAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCC‑CATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATAAGaat                                                                                                                                                     >  2:283412/1‑150 (MQ=255)         ttAAGAGATAGGTAAAAAAGTGCAGCGTTCAGAAATAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCC‑CATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATAAGAATAATCTCAt                                                                                                                                             >  2:87445/1‑150 (MQ=255)                 tAGGTAAAAAAGTGCAGCGTTCAGAAATAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCC‑CATCCGGCGCTTATCTCCGGCACCCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAAc                                                                                                                                    >  2:107404/1‑151 (MQ=255)                      aaaaaaGTGCAGCGTTCAGAAATAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCC‑CATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAACccgcc                                                                                                                               >  1:469683/1‑151 (MQ=255)                        aaaaGAGCAGCGTTCAGAAATAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCC‑CATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAACCCGCCGt                                                                                                                             >  2:601172/1‑151 (MQ=255)                         aaaGTGCAGCGTTCAGAAATAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCC‑CATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAACCCGCCGtt                                                                                                                            >  2:302259/1‑151 (MQ=255)                          aaGTGCAGCGTTCAGAAATAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCC‑CATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAACCCGCCGttt                                                                                                                           <  2:706271/151‑1 (MQ=255)                                   gttaaaaaaaaaaaaaCCCCTTAAGTTTGTGCGACACGGCCTTAAGGTTTTCCCCCC‑CATCCGGCTCTTATCCCCGGCCCTCCCATTGCCTTA‑CTTTTTGAGGGGCCAAAAAAAAAAATTCCATAAACCAAACCCGCCGTTTTAACACaa                                                                                                                   <  1:522316/144‑1 (MQ=255)                                   gTTCAGAAATAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCC‑CATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAACCCGCCGTTTTAACACaa                                                                                                                   >  1:146626/1‑150 (MQ=255)                                    ttCAGAAATAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCC‑CATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAACCCGCCGTTTTAACACAAAc                                                                                                                 >  2:268285/1‑151 (MQ=255)                                          aaTAAAAAACCCTTTAGGTCTGGGCGACACGGGCTTAAGGTTTTCTCCCC‑CACCCGGCGCTTATCCCCGGCCCTCTCGGTGGTTTA‑CCTTTTGAGGGGGCGATAAGAAAAATCTAAAAAAGCTAACCCGCCGTTTTAACACAAACTGCGAt                                                                                                           <  2:607271/151‑1 (MQ=255)                                             aaGAAACCCCTTAAGTCTGTGCGACACAGCCTTAGGGGTTTCCCCCC‑CACCCGGCGCTTACCCCCGCCCCTCCCAGTGGTTTA‑GCTCTTGAGGGGGCAAAAAAAATAATCCAATAAATCTAACCCGCCGTTTTAACACAAACTGCGATTAg                                                                                                        <  2:214310/151‑1 (MQ=255)                                             aaGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCC‑CATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAACCCGCCGTTTTAACACAAACTGCGAtt                                                                                                          >  2:108639/1‑149 (MQ=255)                                               gAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCC‑CATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAACCCGCCGTTTTAACACAAACTGCGATTAGt                                                                                                       >  1:128252/1‑150 (MQ=255)                                                  aaCCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCC‑CATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATGAGAATAATCTCATAAAGCTAACCCGCCGTTTTAACACAAACTGCGATTAGtatt                                                                                                    >  2:466330/1‑150 (MQ=255)                                                    cccTTAGGTCTGTGCGACACAGGCTTAAGGTTTTCTCCCC‑CATCCGGCGCTTATCCCCGGCCCTCTCAGTGGTTTA‑GCTCTTGAGGGGGCGATAAAAATAATCTCATAAAGCTAACCCGCCGTTTTAACACAAACTGCGATTAGTattatt                                                                                                 <  2:590515/151‑1 (MQ=255)                                                      cTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCC‑CATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAACCCGCCGTTTTAACACAAACTGCGATTAGTATTAtttt                                                                                               >  2:684092/1‑151 (MQ=255)                                                         aaGTCTGTGCGACACAGGCTAAAGGTTTTCTCCCC‑CATCCGGCGCTTATCCCCGGCACTCTCAGTGGTTTA‑GCTCTGGAAGGGGCAAAAAAAATAATCTCAAAAAGCTAACCCGCCGTTTTAACACAAACTGCGATTAGTATTAttttt                                                                                              <  2:680411/149‑1 (MQ=255)                                                            tCTGTGCGACACAGGCTTAAGGGTTTCTACCC‑CATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAAc                                                                                          >  2:184635/1‑150 (MQ=255)                                                               gtgCGACACAGGCTTAAGGGTTTCTACCC‑CATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAat                                                                                       >  1:108569/1‑150 (MQ=255)                                                                ggCGGCACGGTCTTAAGGTTTTCTCCCC‑CCCCGAGCTTATATCTCCGTCCCTCT‑AATTGCTTACGCTTTTAAAGGGGAAAAAAAAATAATTTAAAAAACAAAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAatat                                                                                     <  1:554025/150‑1 (MQ=255)                                                                     cacaGGTTTAAGGTTTCCTACCC‑CATCCGGCGCTTATCCCCGGCCCTCTCGGTGGTTTA‑GCTCTTGAAGGGGCAAAAAAAATAATCTCAAAAACCTAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATc                                                                                    <  2:538657/147‑1 (MQ=255)                                                                      acaGGTTAAAGGGTTTCTCCCC‑CACCCGGCGTTTACCCCCGGCCCTCTCAGTGGTTTA‑GCTCTTGAGGGGGCAATAAAAATAATCTAAAAAAGCTAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCg                                                                               <  2:355626/151‑1 (MQ=255)                                                                         gtcTTAAGGGTTTCTCCCC‑CACCCGGCGCTTATCCCCGGCCCCCTCAGTGGCTTA‑GCTCTTGAGGGGGCGAAAAAAAAAATCTCATAAAGCTAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCgg                                                                              <  2:339698/147‑1 (MQ=255)                                                                          gCTTAAGGGTTTCTACCC‑CATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGt                                                                             >  1:343917/1‑149 (MQ=255)                                                                             tAAAGGATTCCACCCGCATCCGGCTTTTATTTCCGCCACTCGCTGTGTTTTA‑GTTCTTGATGGGGAAAAAAAAATAATTACAGAATGCTAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGa                                                                          <  1:293943/150‑1 (MQ=255)                                                                                gtgttccccccc‑cACCGGGCGTTTATCCCCGCCCCTTTTAGTGTTTTA‑GCTTTTGAGGGGGAAATAAAAATAATCTAATAAAAAAAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGa                                                                          <  1:668017/137‑1 (MQ=255)                                                                                    ttcacccc‑cACCCGGCTATTTCCACCGCCCCTCTCAGTGGCTTA‑CCTTTTGAAGGGGCGATAAAAATAATCAAAAAAAACTAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGt                                                                  <  2:117802/145‑1 (MQ=255)                                                                                       tACCC‑CATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCg                                                                               >  1:229366/1‑134 (MQ=255)                                                                                        cccc‑cACCCGGCTCTTATCCCCGCCACTCTCAGTGGTTTA‑GCTTTTGAAGGGGCGAAAAAAATAATCTCATAAAGCTAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCg                                                                               <  2:229401/132‑1 (MQ=255)                                                                                         ccc‑cACCGGGCGCTTATCCCCGCCACTCTAAGTGGTTTA‑GCTTTTGAGGGGGCAAAAAAAATAATCTAAAAAAGAAAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTa                                                                 <  1:69093/146‑1 (MQ=255)                                                                                         ccc‑cACCCGGCGCTAACCTCCGCCACCCTCAGTGGCTTA‑GCTTTTGAAGGGGAAATAAAAATAATCAAAAAAAGCAACCCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTaag                                                            <  1:521623/151‑1 (MQ=255)                                                                                                    cgtttATCCCCGCCCCTCTCAGTGGCTTA‑GCTTTTAAGGGGGAAAAAAAAATAATCTAAAAAAACAAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAgg                                                        <  1:500741/142‑1 (MQ=255)                                                                                                           ctcCGGCACTCACAGTTGTTTA‑GCTTTTGAAGGGGAAAAAAAAATATTCTAAAAAACCAAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGaa                                                <  1:351672/146‑1 (MQ=255)                                                                                                               ggCCCTCTCAGTGGCTTA‑GCTTTTGAGGGGGCAAAAAAAATAATCTCATAAAGCTACCCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACgg                                       <  2:252929/151‑1 (MQ=255)                                                                                                                 cACTCTCAGTGGCTTA‑GCTCTTGTACGGGCGATAAGAATAATCTCCTAACGCTAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGATCCTGGACg                                        >  1:724385/1‑148 (MQ=255)                                                                                                                           ggCTTA‑GCTCTTGAGGGGGCAATAAAAATAATCTAATAAAGCTAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAg                           <  2:69685/151‑1 (MQ=255)                                                                                                                              ttA‑GCTCATGAGGGGGAGATAAAAATAATCGCATAAAGCAAGCCCGCCGGTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAgg                          <  1:62144/149‑1 (MQ=255)                                                                                                                                   tttttGAGGGGGCGATAAAAATAATTCCAAAAAACAAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCa                            <  1:747264/140‑1 (MQ=255)                                                                                                                                    tctTGAAGGGGCGATAAGAATAATCTCATAAAGCTAACCCCCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCGAttt                   >  2:673598/1‑151 (MQ=255)                                                                                                                                      ttGAAGGGGCGATAAGAATAATCTCATAAAGCTAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCGATTTgg                 >  1:750866/1‑151 (MQ=255)                                                                                                                                                     gAATAATCTCATAAAGCTAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCGATTTGGCGAACTTGCGGCAtt  >  2:96507/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                       ATGACTATTTAAGAGATAGGTAAAAAAGTGCAGCGTTCAGAAATAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCC‑CATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTA‑GCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAACCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCGATTTGGCGAACTTGCGGCATT  >  NC_000913/1764628‑1764924

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑