Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,492,028	0	C	T	51.6%	23.9 / 44.0	32	Q90Q (CAG→CAA)	ppiA	peptidyl‑prolyl cis‑trans isomerase A (rotamase A)
Reads supporting (aligned to +/- strand):  ref base C (2/13);  new base T (16/0);  total (19/13)
Fisher's exact test for biased strand distribution p-value = 5.09e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.23e-06

TGGTCAAGGAAGGCGTTATCGGCAACGTTGATAAAGAACTGGCTGGTGGCGCTGTCTTTGTCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGTTTGGTTTTTTCTGCTGCATCTGCTCGGTGAAACCGCCGCCCTGAATCATAAAGCCAGGAATGACGCGGTGAAAGGTAGTGTTGTTATAAAAACCGCTGTTCACATAATCGACAAAGTTTTGCACAGACACTGGCGCTTTTTGTTTATCCAGCTCCAGTT  >  NC_000913/3491882‑3492176                                                                                                                                                    |                                                                                                                                                     tGGTCAAGGAAGGCGTTATCGGCAACGTTGATAAAGAACTGGCTGGTGGCGCTGTCTTTGTCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGGTTTGGTTTTTctg                                                                                                                                                    >  2:11775/1‑149 (MQ=255)       aggaaggCGTTATCGGCAACGTTGATAAAGAACTGGCTGGTGGCGCTGTCTTTGTCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGGTTGGGTTTTTTtgctgcct                                                                                                                                              >  2:177835/1‑147 (MQ=255)             gCGTTATCGGCAACGTTGATAAAGAACTGGCTGGTGGCGCTGTCTTTGTCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGTTTGGTTTTTTTTGCTGCATCTGCTCgg                                                                                                                                      >  2:447467/1‑151 (MQ=255)                     ggCAACGTTGATAAAGAACTGGCTGGTGGCGCTGTCTTTGTCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGGTTGGGTTTTTTTGCTGCCTCTTCTCGGGGaaaac                                                                                                                               >  2:529914/1‑148 (MQ=255)                                tAAAGAACTGGCTGGTGGCGCTGTCTTTGTCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGTTTGGTTTTTTCTGCTGCATCTGCTCGGTGAAACCGCCGCCCTGAAt                                                                                                                   <  2:433804/151‑1 (MQ=255)                                tAAAGAACTGGCTGGTGGCGCTGTCTTTGTCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGTTTGGTTTTTTCTGCTGCATCTGCTCGGTGAAACCGCCGCCCTGAAt                                                                                                                   <  1:440428/151‑1 (MQ=255)                                tAAAGAACTGGCTGGTGGCGCTGTCTTTGTCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGTTTGGTTTTTTCTGCTGCATCTGCTCGGTGAAACCGCAGCCCTGAAt                                                                                                                   <  1:376039/151‑1 (MQ=255)                                    gAACTGGCTGGTGGCGCTGTCTTTGTCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGTTTGGTTTTTTTTGCTGCATCTGCTCGGGGAAAACGCCGCCCTGAATCATa                                                                                                               >  2:348942/1‑151 (MQ=255)                                    gAACTGGCTGGTGGCGCTGTCTTTGTCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGGTTTGTTTTTTTTGCTGCATCTGCTCGGTGAAACCGCCGCCCTGAATCATa                                                                                                               >  1:401159/1‑151 (MQ=255)                                     aaCTGGCTGGTGGCGCTGTCTTTGTCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGTTTGGTTTTTTCTGCTGCATCTGCTCGGTGAAACCGCCGCCCTGAATCATaa                                                                                                              <  1:264685/151‑1 (MQ=255)                                         ggctggTGGCGCTGTCTTTGTCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGTTTTGTTTTTTTTGCTGCATCTGCTCGGTGAAACCGCCGCCCCGAATCATaaaac                                                                                                           >  2:522540/1‑148 (MQ=255)                                               tggCGCTGTCTTTGTCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGTTTGGTTTTTTCTGCTGCATCTGCTCGGTGAAACCGCCGCCCTGAATCATAAAGCCAGGAAt                                                                                                    <  2:529964/151‑1 (MQ=255)                                               tggCGCTGTCTTTGTCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGTTTGGTTTTTTCTGCTGCATCTGCTCGGTGAAACCGCCGCCCTGAATCATAAAGCCAGGAAt                                                                                                    <  1:112718/151‑1 (MQ=255)                                                      gTCTTTGTCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGGTTTGTTTTTTTTGCTGCATCTGCTCGGGGGAAACGCCGCCCTGAATCATAAAACCAGGGATGACGCgg                                                                                             >  1:353637/1‑151 (MQ=255)                                                      gTCTTTGTCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGGTTTGTTTTTTTTCCTGCCTCTGTTCGGGGAAACCGCCCCCCCTAATCATAAAACCCGGAATGAAGCgg                                                                                             >  1:57884/1‑151 (MQ=255)                                                      gTCTTTGTCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGGTTGGGTTTTTTTGCTGCATCTGCTCGGTGGAACCGCCGCCCCGAATTATAAAACCAGGAATGAAGCgg                                                                                             >  1:476122/1‑151 (MQ=255)                                                             tCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGTTTGGTTTTTTCTGCTGCATCTGCTCGGTGAAACCGCCGCCCTGAATCATAAAGCCAGGAATGACGCGGTGAAAg                                                                                       <  1:185092/150‑1 (MQ=255)                                                                     aCGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGTTTGGTTTTTTCTGCTGCATCTGCTCGGTGAAACCGCCGCCCTGAATCATAAAGCCAGGAATGACGCGGTGAAAGGTAGtgttg                                                                              <  2:42646/151‑1 (MQ=255)                                                                          ccATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGGTTGGTTTTTTCTTCTGTTTCTGATCGGGGAAAACGCCGACCTGAATCAAAAAACAAGGAAAGAAACAGAGAAAGAGAGAGGTGTtatt                                                                         >  1:115545/1‑150 (MQ=255)                                                                                  aTGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGTTTGGTTTTTTTTTCTGCATCTGCTCGGGGAAACCGCCCCCCTGAATTATAAAACCAGGGATGACGCGGGGTAAGGGAGTGTTGTTTTAAAAACCg                                                                  >  1:46655/1‑150 (MQ=255)                                                                                     gTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGGTTTGTTTTTTTTGCTGCATCTGCTCGGTGAAACCGCCGCCCTGAATCATAAAACCAGGAATGACGCGGGGAAAGGGAGGGTTGTTATAAAAAACg                                                                  >  2:251156/1‑147 (MQ=255)                                                                                           cgcgTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGCGGGGTTTGGTTTTTT‑TGCTGCCTCTGCTCGGTGGAAACGCCGCCCTGAATCATAAAGCCCGGAATGACGCGGGGGAAGGGAGTGGTGTTTTAAAAAACCCCGTTcacaa                                                        >  1:390913/1‑150 (MQ=255)                                                                                              gtgtTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGGTTGGTTTTTTTTGCTGCATCTGCTCGGTGAAAACGCCGCCCTGAATCATAAAACCAGGAATGACGCGGGGGAAGGTAGGGTTGTTTTAAAAACCGCAGTTCACATAAt                                                     >  2:94588/1‑151 (MQ=255)                                                                                              gtgtTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGGTTGGTTTTTTTTGCTGCATCTGCTCGGGGAAACCGCCGCCCTGAATCATAAAACCAGGGATGACGCGGTGGAAGGGAGTGTTGTTTTAAAAAACGCTGTTCACATAAt                                                     >  2:502899/1‑151 (MQ=255)                                                                                                        ggCCGTTATCGGCTTCATTTTTGATTGGC‑GGGTTTGGGTTTTTTTGCTGCATCTGCTCGGTGAAAACGCCGCCCTGAATCATAAAACCAGGAATGACGCGGGGAAAGGGAGGGTTGTTATAAAAACCGCTGTTCACATAATCGACAAAGtt                                           >  2:101317/1‑151 (MQ=255)                                                                                                        ggCCGTTATCGGCTTCATTTTTGATTGGC‑GGGGTTGGTTTTTTTTGCTGCATCTGCTCGGTGGAACCGCCGCCCTGAATCATAAAACCAGGGATGACGCGGTGGAAGGGAGTGGTGTTATAAAAAACGCTGTTTACATAAACGACAAAggt                                           >  1:438811/1‑149 (MQ=255)                                                                                                        ggCCGTTATCGGCTTCATTTTTGATTGGC‑GGGGTTGGTTTTTTCTTCTGGCTCTGCCCGGGGAAACCCCCGCCCTGAATCATAAAGCGAGGAATGAGACGGTGTGAAGTATTGTGGTTTTAAAAAACGCGGTTCACATAATCGACaaaagt                                           >  2:79839/1‑148 (MQ=255)                                                                                                         gCCGTTATCGGCTTCATTTTTGATTGGC‑GGGGTTGGGTTTTTTTGCTGCATCTTCTCGGGGGAACCGCCGCCCCGAATCATAAAACCAGGAATGACGCGGGGAAAGGGAGGGTTGTTATAAAAAACGCTGTTCACATAATCGACAAAAttt                                          >  2:470734/1‑151 (MQ=255)                                                                                                              tATCGGCTTCATTTTTGATTGGC‑GGGTTTGGTTTTTTCTGCTGCATCTGCTCGGTGAAACCGCCGCCCTGAATCATAAAGCCAGGAATGACGCGGTGAAAGGTAGTGTTGTTATAAAAACCGCTGTTCACATAATCGACAAAGTTTTGcac                                     <  1:123093/151‑1 (MQ=255)                                                                                                              tATCGGCTTCATTTTTGATTGGC‑GGGTTTGGTTTTTTCTGCTGCATCTGCTCGGTGAAACCGCCGCCCTGAATCATAAAGCCAGGAATGACGCGGTGAAAGGTAGTGTTGTTATAAAAACCGCTGTTCACATAATCGACAAAGTTTTGcac                                     <  2:218341/151‑1 (MQ=255)                                                                                                                                         tttggtttTTTCTGCTGCATCTGCTCGGTGAAACCGCCGCCCTGAATCATAAAGCCAGGAATGACGCGGTGAAAGGTAGTGTTGTTATAAAAACCGCTGTTCACATAATCGACAAAGTTTTGCACAGACACTGGCGCTTTTTGTTTATcc            <  1:321484/150‑1 (MQ=255)                                                                                                                                         tttggtttTTTCTGCTGCATCTGCTCGGTGAAACCGCCGCCCTGAATCATAAAGCCAGGAATGACGCGGTGAAAGGTAGTGTTGTTATAAAAACCGCTGTTCACATAATCGACAAAGTTTTGCACAGACACTGGCGCTTTTTGTTTATcc            <  2:372333/150‑1 (MQ=255)                                                                                                                                                  ttCTGCTGCATCTGCTCGGTGAAACCGCCGCCCTGAATCATAAAGCCAGGAATGACGCGGTGAAAGGTAGTGTTGTTATAAAAACCGCTGTTCACATAATCGACAAAGTTTTGCACAGACACTGGCGCTTTTTGTTTATCCAGCTCCAGtt  <  2:390922/151‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                     TGGTCAAGGAAGGCGTTATCGGCAACGTTGATAAAGAACTGGCTGGTGGCGCTGTCTTTGTCAGCGGTACGTGCCATCGCGATGGTGCCACGCGTGTTGCGCAGGCCGTTATCGGCTTCATTTTTGATTGGC‑GGGTTTGGTTTTTTCTGCTGCATCTGCTCGGTGAAACCGCCGCCCTGAATCATAAAGCCAGGAATGACGCGGTGAAAGGTAGTGTTGTTATAAAAACCGCTGTTCACATAATCGACAAAGTTTTGCACAGACACTGGCGCTTTTTGTTTATCCAGCTCCAGTT  >  NC_000913/3491882‑3492176

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑