Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,556,207	0	T	C	51.8%	15.9 / 35.9	28	S215G (AGT→GGT)	rtcA	RNA 3'‑terminal phosphate cyclase
Reads supporting (aligned to +/- strand):  ref base T (12/1);  new base C (0/14);  total (12/16)
Fisher's exact test for biased strand distribution p-value = 7.48e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.03e-05

GCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCCACCAC  >  NC_000913/3556074‑3556354                                                                                                                                      |                                                                                                                                                    ataagagccattttttCCCCGACGAAAAAAAAGCGTTCGGTGATTTTTTCACTTTCGACTTCAAGCGAGACGGTTTTCCCCGGCCCCTGGTCGCGCGGCAGTTTATAAATATTCTGTTCATGCAGGAAAAAACCCCCCGCCAGTGTAGCGa                                                                                                                                    <  1:479810/139‑1 (MQ=255)       ccgcgTTTTTCACCGACAAAAAAAAAGCGTTCGGTGATATTTTCCCTTTCGACTTCAAGCGAGACGGTTTCCCCCGCCCCCGGGCCGCGCGGCAGTTTAGAAATTTTCTGTTCATGCAGGGAAAACCCCCCCGCCAGTGTAGCGATTTCa                                                                                                                               <  1:47370/149‑1 (MQ=255)            cTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAACTCCCCGCCAGTGTAGCGa                                                                                                                                    >  2:479816/1‑140 (MQ=255)            cTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCa                                                                                                                         >  1:116169/1‑151 (MQ=255)              tttCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAg                                                                                                                        >  1:104334/1‑150 (MQ=255)                 ccccGACGACAAAAAAGCGTTCGGTGATTTTTTCACTTTCGACTTCAAGCGAGACGTTATTCCCCGGCCCCGGGTCGCGCGGCGGTTTATGAATATTCTGTTCATGCAGGAAAAAACCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAAc                                                                                                                    <  2:412337/149‑1 (MQ=255)                   ccgccgAAAAAAAAGCGTGCGGTAATTTTTCCCCTTCCGACTTCAAGCGAGACGGTATCCCCCGGCCCCGGGCCGCGCGGCAGTTTATGAATATTCTGTTCAGGCAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACAt                                                                                                                  <  1:312217/151‑1 (MQ=255)                      ccgaaAAAAAAGCGTTCGGTGATATTTCCCCTTTCGCCTTCAAGCGAGACGGTATTCCCCGCCCCCTGCCCCCGCGCCAGTTTATGAATTTTCTTTTCATGCAGGGAAAAACCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATgg                                                                                                                <  1:225067/149‑1 (MQ=255)                            aaaaaGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGca                                                                                                         >  2:150491/1‑151 (MQ=255)                                            ttttttCTCTTTCGATTCCAAGCGAGGCGGTATTGCCCGCCCCGTGGTCGCGCGGCAGGTTATGAATATTTTTTTCAGGCAGGGAAAAACGCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAAc                                                                                         <  2:404356/149‑1 (MQ=255)                                                              cAAGCGAGCCGTTATCCCCCGCCCCCTGGCCGCGCGGCAGTTTATGAATTTTCTGTTCATGCAGGGAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGcac                                                                       <  1:263364/151‑1 (MQ=255)                                                              cAAGCGAGACGGTATTCCCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGAAAAAACCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGcac                                                                       <  2:135439/151‑1 (MQ=255)                                                              cAAGCGAGACGGTATTCCCCGGCCCCGGGCCGCGCGGCAGTTTATAAATATTCTGTTCATGCAGGAAAAAACCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGcac                                                                       <  2:228263/151‑1 (MQ=255)                                                                    agaCGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGtt                                                                 >  2:144193/1‑151 (MQ=255)                                                                    agaCGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGtt                                                                 >  1:356784/1‑151 (MQ=255)                                                                    agaCGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGtt                                                                 >  1:217205/1‑151 (MQ=255)                                                                         gTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCcg                                                             >  2:612595/1‑150 (MQ=255)                                                                                                   aaGGTTAGGAATTTCCTTTCCATGAAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAAc                                  <  1:177252/150‑1 (MQ=255)                                                                                                     ggTTATGAATATTCTGTTCATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGa                                >  1:325255/1‑151 (MQ=255)                                                                                                      gTTATAATTATCCGGTTCAGGCAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAAc                                  <  1:310807/148‑1 (MQ=255)                                                                                                      gTTATAAATTTTCTGTTCAGGCAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAAc                                  <  1:312675/148‑1 (MQ=255)                                                                                                        tATGAATATTCTGTTCATGCAGGAAAAACCTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGc                             <  2:152244/151‑1 (MQ=255)                                                                                                           gAATATTCTGTTCATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCa                           >  1:406867/1‑150 (MQ=255)                                                                                                              tttccTGTTCAGGCGGGGAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACggg                       <  1:159835/147‑1 (MQ=255)                                                                                                                    tttCATGAAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGAc                 <  2:61530/150‑1 (MQ=255)                                                                                                                               gAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGcca      >  2:149957/1‑151 (MQ=255)                                                                                                                               gAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGcca      >  2:667516/1‑151 (MQ=255)                                                                                                                                   aaCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCcaccac  <  2:667946/151‑1 (MQ=255)                                                                                                                                      |                                                                                                                                                    GCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCCACCAC  >  NC_000913/3556074‑3556354

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: ‑