Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	541,284	0	A	G	41.5%	59.1 / 14.1	42	G240G (GGA→GGG)	ybbY	putative uracil/xanthine transporter
Reads supporting (aligned to +/- strand):  ref base A (1/23);  new base G (17/0);  total (19/23)
Fisher's exact test for biased strand distribution p-value = 1.19e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGTTTTGCCCGTTATGGCCTGCTGGTCGGCACCATAACCGGCTGGTTGTTGTGGTACTTTTGCTTTCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGCAGCAGGGCGCAGGGAATACGCGTTATCGTCGTAGCTTTGTGGCGACCGGATTTATGACGCTGATA  >  NC_000913/541140‑541434                                                                                                                                                 |                                                                                                                                                         aCGTTTTGCCCGTTATGGCCTGCTGGTCGGCACCATAACCGGCTGGTTGTTGTGGTACTTTTGCTTTCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAattatt                                                                                                                                                    <  2:317608/151‑1 (MQ=255)  cGTTTTGCCCGTTATGGCCTGCTGGTCGGCACCATAACCGGCTGGTTGTTGTGGTACTTTTGCTTTCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGGGCTTTTTTGCCGGGGgttatt                                                                                                                                                    >  2:549264/1‑150 (MQ=255)   gTTTTGCCCGTTATGGCCTGCTGGTCGGCACCATAACCGGCTGGTTGTTGTGGTACTTTTGCTTTCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGGGCTTTGTCGGCGGGCATTATTCt                                                                                                                                                  >  2:510681/1‑151 (MQ=255)      ttGCCCGTTATGGTCTGCTGGTCGGCACCATAACCGGCTGGTTGTTGTGGTACTTTTGCTTTCCTTCTTCGCACGCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAATGATTCt                                                                                                                                                  <  2:83764/148‑1 (MQ=255)           cGTTATGGCCTGCTGGTCGGCACCATAACCGGCTGGTTGTTGTGGTACTTTTGCTTTCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGGATTTTTTTTAcggcgg                                                                                                                                          >  1:467891/1‑151 (MQ=255)             ttATGGCCTGCTGGTCGGCACCATAACCGGCTGGTTGTTGTGGTACTTTTGCTTTCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGGTTTGTCGCCGGGGATTATTCTGAcggcgggg                                                                                                                                        >  1:113759/1‑149 (MQ=255)              tATGGCCTGCTGGTCGGCACCATAACCGGCTGGTTGTTGTGGTACTTTTGCTTTCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGGGGTTTTTCGCCGGGGATTTTTTTGCcggcgggg                                                                                                                                        >  2:17534/1‑148 (MQ=255)              tATGGCCTGCTGGTCGGCACCATAACCAGCTGGTTGTTGTGGTACTTTTGCTTTCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAATTATTCTGACGGCGGTg                                                                                                                                        <  1:518824/150‑1 (MQ=255)                 ggCCTGCTGGTCGGCACCATAACCGGCTGGTTGTTGTGGTACTTTTGCTTTCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAATTATTCTGACGGCGGTGATTa                                                                                                                                    <  2:725909/151‑1 (MQ=255)                   ccTGCTGGTCGGCACCATAACCGGCTGGTTGTTGTGGTACTTTTGCTTTCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCGTTTTCGCCGGGGATTATTTTGGcggcgggg                                                                                                                                        >  2:26496/1‑143 (MQ=255)                          gTCGGCACCATAACCGGCTGGTTGTTGTGGTACTTTTGCTTTCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑gg                                                                                                                          <  2:141250/151‑1 (MQ=255)                                  cATAACCGGCTGGTTGTTGTGGTACTTTTGCTTTCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATc                                                                                                                  <  2:573478/151‑1 (MQ=255)                                              gttgttGTGGTACTTTTGCTTTCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTTTCGCCGGGGATTATTTTGACGGCGGGGGTTTCAGGGCT‑GGGAAATATTAACaaaa                                                                                                           >  1:222205/1‑144 (MQ=255)                                                      ggTACTTTTGCTTTCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTTTTGCCGGGGATTATTCTGACGGCGGGGGTTTCAGGGCT‑GGGAAATAAcaacaaaaactcacg                                                                                                    >  1:480516/1‑136 (MQ=255)                                                          cTTTTGCTTTCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTc                                                                                           <  2:392054/149‑1 (MQ=255)                                                              tGCTTTCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTTCTTTTTCGCCGGGGATTTTTTTTAACGCGGGGAATTCACGGCTCGGTAAA‑ATCAACAAAACCC‑ACCGGGCGATTTgggg                                                                                       >  1:353918/1‑149 (MQ=255)                                                              tGCTTTCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGGATTATTCTGACGGCGGGGGTTACAGGGCT‑GGTAAATATTAACAAAACCC‑ACGGGGCGGTTCgggg                                                                                       >  1:518491/1‑149 (MQ=255)                                                                   tCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTTTCGCCGGGGATTATTTTGACGGCGGGGGGTTAAGGGGT‑GGTAAATATTAGCAAAAACT‑ACCGTGCGGTTTgggggaaggcg                                                                                >  2:625860/1‑144 (MQ=255)                                                                    ccTTCTTCGCACTCGCTCTCCGGTGAGTTGCCCTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATTCCT‑ACGGTGCGATTCGGGGCACGGAt                                                                                <  1:388895/150‑1 (MQ=255)                                                                       tcttcGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGtt                                                                             <  2:133213/150‑1 (MQ=255)                                                                          tcGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTTTCGCCCGGGATTATTTTGACGGCGGGGGTTTAAGGGGT‑GGGGAAAATTAGCAAAAACC‑ACCGGGCGGGTTGGGGGGCGGGTGtttttt                                                                         >  1:691474/1‑151 (MQ=255)                                                                            gCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGGAATTTTCTGTCGGGGGGGGTTACAAGGCTGGGTAAAAATCA‑CAATACCTCACGGGGGGATTTGGGG‑GCGGGTGtttttt                                                                         >  1:322924/1‑149 (MQ=255)                                                                                  gCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGGTTTTTCTCCCGGGAATATTCTCACGGCGGGGGTTAAAGGTGT‑GGTATCAATCAACAATAACC‑ATGGGGCGGGTCGGGGGACGGGGGttttttt                                                                        >  2:416099/1‑143 (MQ=255)                                                                                  gCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGGATTATTTTGACGGCGGGGGTTTCAGGGCT‑GGGAAAAATCAGCAAAAACT‑ACGGGGCGGTTCGGGGGACGGGTGtttttttt                                                                       >  1:469276/1‑143 (MQ=255)                                                                                       ccGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGcagcag                                                              <  1:550654/149‑1 (MQ=255)                                                                                        cGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGGATTATTTTGTCGGCGGGGGGTACAGGGCT‑GGGGAAAATTAGCCATAACT‑ACGGGGGGGTTTGGGGGACGGGAGTTTTTTTTTCGCCGCAgggg                                                           >  1:157483/1‑150 (MQ=255)                                                                                            gAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGCAGCAGGGCGCAg                                                       <  2:557127/151‑1 (MQ=255)                                                                                                 gCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGCAGCAGGGCGCAGGGaa                                                   <  1:518614/150‑1 (MQ=255)                                                                                                  cACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGCAGCAGGGCGCAGGGAATa                                                 <  1:523850/151‑1 (MQ=255)                                                                                                   aCTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTTTCGCCGGGGATTTTTCTGACGGCGGGGGTTTCAAGGCT‑GGTAAATATCAACCAAACCC‑ACCGGGCGGTTCGGGGGACGGGTTTTTTTTTTTCCCCGCAGGGGGCAggggaaa                                                 >  1:325171/1‑146 (MQ=255)                                                                                                       gCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTTTCGCCGGGGATTATTTTGACGGCGGGGGTTACAGGTCT‑TGGAAATATTAGCAATACCC‑ACGGGGGGGTTTGGGGGCCGGGTGTTTTTTTTTCGCCGCAGGGGGCCggggaaaagcg                                             >  1:262490/1‑142 (MQ=255)                                                                                                        cAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGCAGCAGGGCGCAGGGAATACGCGtt                                           <  1:5676/151‑1 (MQ=255)                                                                                                          gTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGCAGCAGGGCGCAGGGAATACGCGTTAt                                         <  1:536634/151‑1 (MQ=255)                                                                                                            ggTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGCAGCAGGGCGCAGGGAATACGCGTTAtc                                        <  1:544054/150‑1 (MQ=255)                                                                                                            ggTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGCAGCAGGGCGCAGGGAATACGCGTTAtc                                        <  2:506905/150‑1 (MQ=255)                                                                                                                                ggTGCTTTGTCGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGCAGCAGGGCGCAGGGAATACGCGTTATCGTCGTAGCTTTGTGGCGAc                     <  2:103670/149‑1 (MQ=255)                                                                                                                                   gCTTTGTCGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGCAGCAGGGCGCAGGGAATACGCGTTATCGTCGTAGCTTTGTGGCGACCGGAt                <  1:593940/151‑1 (MQ=255)                                                                                                                                        gTCGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGCAGCAGGGCGCAGGGAATACGCGTTATCGTCGTAGCTTTGTGGCGACCGGATTTATg           <  1:353140/151‑1 (MQ=255)                                                                                                                                          cGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGCAGCAGGGCGCAGGGAATACGCGTTATCGTCGTAGCTTTGTGGCGACCGGATTTATGAc         >  1:67517/1‑151 (MQ=255)                                                                                                                                             cGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGCAGCAGGGCGCAGGGAATACGCGTTATCGTCGTAGCTTTGTGGCGACCGGATTTATGACGCt      <  2:210739/151‑1 (MQ=255)                                                                                                                                             cGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATACCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGCAGCAGGGCGCAGGGAATACGCGTTATCGTCGTAGCTTTGTGGCGACCGGATTTATGACGCt      <  1:272640/151‑1 (MQ=255)                                                                                                                                               ggAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGCAGCAGGGCGCAGGGAATACGCGTTATCGTCGTAGCTTTGTGGCGACCGGATTTATGACGCTGa    <  1:625850/151‑1 (MQ=255)                                                                                                                                                 aaTTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGCAGCAGGGCGCAGGGAATACGCGTTATCGTCGTAGCTTTGTGGCGACCGGATTTATGACGCTGAt   >  1:138250/1‑150 (MQ=255)                                                                                                                                                 aaTTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGCAGCAGGGCGCAGGGAATACGCGTTATCGTCGTAGCTTTGTGGCGACCGGATTTATGACGCTGATa  <  2:453854/151‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                         ACGTTTTGCCCGTTATGGCCTGCTGGTCGGCACCATAACCGGCTGGTTGTTGTGGTACTTTTGCTTTCCTTCTTCGCACTCGCTCTCCGGTGAGTTGCACTGGCAGTGGTTCCCGCTCGGCAGTGGCGGTGCTTTGTCGCCGGGAATTATTCTGACGGCGGTGATTACAGGTCT‑GGTAAATATCAGCAATACCT‑ACGGTGCGATTCGGGGCACGGATGTTTTTTATCCGCAGCAGGGCGCAGGGAATACGCGTTATCGTCGTAGCTTTGTGGCGACCGGATTTATGACGCTGATA  >  NC_000913/541140‑541434

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑