Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,434,882	0	T	G	51.4%	32.5 / 54.4	35	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
Reads supporting (aligned to +/- strand):  ref base T (4/13);  new base G (18/0);  total (22/13)
Fisher's exact test for biased strand distribution p-value = 1.61e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.22e-06

CCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATAT  >  NC_000913/2434738‑2435032                                                                                                                                                 |                                                                                                                                                       ccATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAAATCCTACCCGGCAGGGGAATc                                                                                                                                                    >  2:306813/1‑149 (MQ=255)        tGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGa                                                                                                                                            <  1:103976/150‑1 (MQ=255)         gCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCGGCCAGGGGGATCCAACCCGAcc                                                                                                                                          >  1:492106/1‑151 (MQ=255)               gCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCGGTCAGGGGAATCCACCGCGACCAGATa                                                                                                                                     >  1:409195/1‑150 (MQ=255)                  ttGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCCGTCCGGGGAATCCCCcgccgccccgtacaac                                                                                                                                 >  1:77708/1‑138 (MQ=255)                      aCTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGACGGTTTTGGGAGATCATAACGGTCAGGGGAATCCAACGCGCACAGATAAAGACCtt                                                                                                                             >  2:182490/1‑151 (MQ=255)                         cGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCGGTCAGGGGAATCCACCCCGACCCGATACAGCCCCTcc                                                                                                                           >  1:612735/1‑150 (MQ=255)                          gTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGc                                                                                                                         <  1:498038/151‑1 (MQ=255)                                        tGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGGAATCCACCGCGACCAGATACAGCCCTTCCGCCTTTGCCggt                                                                                                               >  1:228285/1‑145 (MQ=255)                                             cTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCGGTCAGGGGAATCCAACGCGACCAAATACAACCCTTCCCCTTTTTCCGTTTCTtccccc                                                                                                      >  1:435945/1‑151 (MQ=255)                                              tACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCGGGCAGGGGAATCCACCCCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTgccccc                                                                                                      >  1:677877/1‑150 (MQ=255)                                                 gTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGCTTTTGGAGATCATACCGGTCAGGGGAATCCACCCCGCCCAGATACAGCCCTTCCCCTTTTTCCGTTGCTGccgcccgc                                                                                                   >  2:423553/1‑150 (MQ=255)                                                   tGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCGGTCAGGGGAATCCACCCCGAACAGATACAGCCCTTCCCCTTTTTCCGTTGCTGCCGCCAGc                                                                                                   >  1:699902/1‑148 (MQ=255)                                                          aGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGGAATCCACCCCGACCAGATACAGCCCTTCCGCTTTTTCCGTTGCTGCCGCCCGCGTTCTGTcc                                                                                          >  1:123233/1‑150 (MQ=255)                                                           gCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCGGGCAGGGGAATCCACCGCGACCCGATACAGCCCTTCCGCTTTTTCCGTTGCTGCCGCCAGCGTTCTGTCCtt                                                                                        >  1:181729/1‑151 (MQ=255)                                                                 aaTGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCGGGCAGGGGAATCCACCCCGACCAGATAAAGCCCCTCCCCCTTTTCCGTTGTTGCCGCCAGCGGTCTTTCCTTTtcccc                                                                                  >  2:316956/1‑149 (MQ=255)                                                                       ccGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCaa                                                                            <  1:662687/151‑1 (MQ=255)                                                                            cATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTg                                                                       <  2:104965/151‑1 (MQ=255)                                                                             attattCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATTATACCGGGCAGGGGAATCCACCGCGGCCAGATACAGCCCTTCCGCTTTTTCCGTTGCTGCCCCCCGCCGTCTGTCCTTTGCCGCCAGc                                                                              >  2:382337/1‑143 (MQ=255)                                                                               tattCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCGGTCAGGGGAATCCACCCCGACCAGATACAGCCCTTCCGCTTTTTCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCt                                                                     >  2:419164/1‑150 (MQ=255)                                                                                     cGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATcc                                                                 <  1:646925/148‑1 (MQ=255)                                                                                             cGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGGAGATCATACCGGGCAGGGGAATCCACCGCGGCCAGATAAAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCCGCGTTCTGTCCTTTGCCGCCAGCAAATCTGCTATCCAGCTCTCCgg                                                       >  1:702863/1‑150 (MQ=255)                                                                                                 aGAAATAGCGGGCCCATTGGCGGTTTTGGGAGATCATACCGGGCAGGGGAATCCACCCCGACCAGATACAGCCCTTCCGCTTTTTGCGTTGCTGCCGCCAGCGGTTTGTCCTTTGCCGCCCGCAACTCTGCTATCCAGCTCTCCGGCTgg                                                   >  1:379343/1‑150 (MQ=255)                                                                                                       aGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTggg                                            <  2:678848/151‑1 (MQ=255)                                                                                                                   ggCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTcc                                 <  2:456604/150‑1 (MQ=255)                                                                                                                   ggCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTcc                                 >  2:97351/1‑150 (MQ=255)                                                                                                                     cGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATc                              >  1:239714/1‑151 (MQ=255)                                                                                                                       gTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATc                              >  1:574872/1‑149 (MQ=255)                                                                                                                       gTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAg                            <  2:475580/151‑1 (MQ=255)                                                                                                                                 aTCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACa                  <  1:321676/151‑1 (MQ=255)                                                                                                                                   cATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAat                <  1:391185/151‑1 (MQ=255)                                                                                                                                      aCCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAatat              <  2:612543/150‑1 (MQ=255)                                                                                                                                       ccGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTc            <  2:609356/151‑1 (MQ=255)                                                                                                                                          gTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTg         >  1:93155/1‑151 (MQ=255)                                                                                                                                          gTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTg         <  1:316988/151‑1 (MQ=255)                                                                                                                                                 tAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCatat  >  2:396860/1‑151 (MQ=255)                                                                                                                                                 |                                                                                                                                                       CCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACAGCCCTTCCGCTTTTGCCGTTGCTGCCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTGACCATAT  >  NC_000913/2434738‑2435032

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑