Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,423,290	0	A	C	44.0%	41.2 / 23.1	50	intergenic (+96/+133)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
Reads supporting (aligned to +/- strand):  ref base A (4/24);  new base C (18/4);  total (22/28)
Fisher's exact test for biased strand distribution p-value = 2.04e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAAATCAGAGCGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGAT‑AAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTT  >  NC_000913/3423149‑3423435                                                                                                                                               |                                                                                                                                                      tAAATCAGAGCGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGGGGTCCTCCCCCCCCCCCCCCg                                                                                                                                                >  1:467643/1‑150 (MQ=255)  aaaTCAGAGCGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCggg                                                                                                                                              <  1:63136/150‑1 (MQ=255)   aaTCAGAGCGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGGGGTCCGCCCCCCCCCCCCCggg                                                                                                                                              >  2:296598/1‑149 (MQ=255)      cAGAGCGTACGAGGGAATTTTTAGCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAACCAAAACGGCCATCCTTCCGGATGGCCTTTCGCTTGATTTGTTGTTTGGCAGTTTATGGC‑GGGCTTCCGGCCCGCGCCCCTCCGGGCC‑G‑tt                                                                                                                                       <  1:735748/151‑1 (MQ=255)       agagCGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGGGGCCTGCCCCCCACCCTCCcgg                                                                                                                                              >  2:250704/1‑145 (MQ=255)       agagCGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCCGCCCCCCCCCCCCCCGGcc                                                                                                                                            >  2:209676/1‑147 (MQ=255)               cGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑a                                                                                                                              <  2:179578/150‑1 (MQ=255)                   ggCATTTTTATCGCAGTTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGtt                                                                                                                         <  2:437991/151‑1 (MQ=255)                   ggCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGGGTCCTGCCCGCCCCCCTCCCGGGC‑G‑TTGCTTCGC‑aaactt                                                                                                                         >  2:519068/1‑147 (MQ=255)                     cATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTGCTGCCCCCCACCCCCCCGGGC‑G‑CTGCTTctgcaaggt                                                                                                                          >  1:670886/1‑141 (MQ=255)                     cATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCa                                                                                                                       <  1:109223/151‑1 (MQ=255)                      aTTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGGCCTGCCCGCCCCCCCCCCGGCC‑G‑CTGCTTCCC‑CACGtt                                                                                                                         >  2:56919/1‑148 (MQ=255)                         tttATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCCCCCCCCTCCGGGCC‑G‑Gttcttctccaaagtcaaa                                                                                                                      >  1:322739/1‑137 (MQ=25)                                  ggTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCcgg                                                                                                          <  2:713750/151‑1 (MQ=255)                                  ggTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCcg                                                                                                           <  1:38671/150‑1 (MQ=255)                                     aaTCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCcggcg                                                                                                        <  2:721032/150‑1 (MQ=255)                                     aaTCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCCGCCTGCCCCCCCCCCCCCCGGCC‑C‑TTGCTTTGC‑CACGTTTAAATCCCCTCCccgc                                                                                                         >  2:482481/1‑149 (MQ=255)                                      aTCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCCCCCCCCTCCCGGCC‑G‑GTGCTTTGC‑AACGTTCCAATCCGCCCCccgcggg                                                                                                      >  2:142249/1‑150 (MQ=21)                                       tCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCCCCCCCCTCCCGGGC‑G‑TTGCTTTGC‑AAAGGTTAAATCCGCCCCcggcgg                                                                                                       >  2:416333/1‑149 (MQ=21)                                        ccATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTCCGGATTGCTTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGAt                                                                                                     <  1:569854/150‑1 (MQ=255)                                           ttAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCCGCCCGCCCCCCCCCCCCCCGGCC‑GTTTGTTTCCC‑AAC‑TTTAAATCCCCCCCccgcggcgtt                                                                                                   >  1:11896/1‑145 (MQ=255)                                                tGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCCGCCCCCCACCCCCCCGGCC‑G‑TTGCTTTGC‑AACGTTTAAATCCCCCCCCCGCGGGTTTGt                                                                                                 >  2:170855/1‑146 (MQ=18)                                                tGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGGCCCGCCCGCCCCCCCCCGCGCC‑G‑GTGCTTTGCAAACGTTCAAA‑CCGCTCCCCGCGGGCTTGttc                                                                                               >  1:794858/1‑146 (MQ=255)                                                 gAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACt                                                                                           <  1:3691/151‑1 (MQ=255)                                                 gAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACt                                                                                           <  2:174925/151‑1 (MQ=255)                                                  aaTGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTc                                                                                          <  2:657520/151‑1 (MQ=255)                                                        aGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCCCCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGgaga                                                                                    <  1:395652/151‑1 (MQ=255)                                                                  gCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAACTCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCg                                                                          <  2:87451/151‑1 (MQ=255)                                                                    aaaaaGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGa                                                                         <  1:251459/150‑1 (MQ=255)                                                                    aaaaaGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGGCCTGCCCCCCCCCCCCCCGGCC‑G‑GTGCTTCCC‑AACGTTCAAATCCCCCCCCCCCGGGTTTTTCCTTCCCGGGGGGGGGTTTAcc                                                                           >  2:450091/1‑148 (MQ=255)                                                                    aaaaaGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGGCCTGCCCCCCCCCCCCCCGGCC‑G‑CTGCTTCGC‑CACCGTCACAATCGCCCCCCGCGGATTTTTGCTTCTCCGGggaggggttgc                                                                            >  1:827678/1‑140 (MQ=255)                                                                           ccATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTTCCCCCCCCCCCCCCGGCC‑C‑TTGCTTTTC‑CACGTTCAAAACCGCTCCCCGCGGGGTTTTGCTACTCCGGAGAGTGTTCACCCccaaaaaa                                                                  >  2:93463/1‑150 (MQ=17)                                                                             aTCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCCGCCCCCCCCCCCCCCCGCC‑G‑TTGCTTCGC‑AACCTTCAAATCCGCTCCCCGCGGCGTTGTCCTTCTCCGGGGAGGGGTCACCCac                                                                        >  1:122236/1‑142 (MQ=14)                                                                               ccTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGGCCCCCCCCCCCCCCTCCGGGCC‑G‑TTGCTTCGC‑AACGGTCAAATCCGCCCCCCGCGGGGTTTTCCTTCTCGGGGGAGTGGTTACCCaccaacaa                                                                  >  2:570747/1‑146 (MQ=17)                                                                                   tCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑TGGCGTCCTGCCCGCCCCCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTCCTCGGGAGAGTGTTCACCGACAAACAACAGAT‑aaa                                                         <  2:804505/150‑1 (MQ=255)                                                                                        tGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGGCCTGCCCCCCCCCCCCCCGGCC‑G‑TTGCTTTTC‑AACGTTCCAATCCCCCCCCCCCGGGGTTTTCCTACTCCGGGGAGGGTTTTCCGACAAACAACAGAT‑aaaaaaaa                                                    >  1:397266/1‑150 (MQ=255)                                                                                         ggCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGAT‑AAAACaaaa                                                   <  2:707348/150‑1 (MQ=255)                                                                                         ggCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGAT‑AAAACaaaa                                                   <  1:450057/150‑1 (MQ=255)                                                                                                cGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGAT‑AAAACAAAAGGCCCAg                                            <  2:706368/150‑1 (MQ=255)                                                                                                 gCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCCTCCTGCCCCCCACCCCCCCGGGC‑G‑TTGGTTCTC‑AACGTTCAAAATCCCTCCCCGCCGGTTTGTTCTACTCTGGGGAGCGTTTACCGAAAAAAAACAAAG‑AAAACaaaaaaccccggc                                          >  2:102797/1‑142 (MQ=255)                                                                                                          gatGTCTGGCAGTTTATGGC‑GGGGGTCCCGCCCCCCCCCCCCCCGGCCGG‑TTGCTCGCC‑ACCGTTAAATCCCCCCCCCGCCGGATTT‑TCCCTCTCCGGGGGGGGGTTTCCCCCAAAAAACAGATAAAAAAAAAAGGCCAAGtttcc                                       >  1:532836/1‑142 (MQ=255)                                                                                                          gatGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGAT‑AAAACAAAAGGCCCAGTCTTCCGACTg                                 <  1:692558/151‑1 (MQ=38)                                                                                                          gatGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGAT‑AAAACAAAAGGCCCAGTCTTCCGACTg                                 <  1:553577/151‑1 (MQ=38)                                                                                                            tGTCTGGGAGTTGATGGC‑GGGCGTCCTGCCCGCCCCCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGAT‑AAAACAAAAGGCCCAGTCTTCCGACTGa                                <  1:758616/150‑1 (MQ=255)                                                                                                             gTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGAT‑AAAACAAAAGGCCCAGTCTTCCGACTGAGc                              <  1:748690/151‑1 (MQ=37)                                                                                                                 ggCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGAT‑AAAACAAAAGGCCCAGTCTTCCGACTGAGCCttt                          <  1:793195/151‑1 (MQ=35)                                                                                                                               gggcgTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGAT‑AAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGAt             <  2:283750/151‑1 (MQ=38)                                                                                                                                   gTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGAT‑AAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCt         <  1:651180/151‑1 (MQ=40)                                                                                                                                   gTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGAT‑AAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCt         <  1:546684/151‑1 (MQ=40)                                                                                                                                          ccGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGAT‑AAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGtt  <  2:116405/151‑1 (MQ=40)                                                                                                                                               |                                                                                                                                                      TAAATCAGAGCGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGC‑GGGCGTCCTGCCCGCCACCCTCCGGGCC‑G‑TTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGAT‑AAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTT  >  NC_000913/3423149‑3423435

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑