Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	29,496	0	T	A	47.2%	31.2 / 25.4	36	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
Reads supporting (aligned to +/- strand):  ref base T (16/3);  new base A (0/17);  total (16/20)
Fisher's exact test for biased strand distribution p-value = 1.35e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGG  >  NC_000913/29354‑29642                                                                                                                                                  |                                                                                                                                                   aaaTTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATc                                                                                                                                            <  2:414319/151‑1 (MQ=255)     tttGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCg                                                                                                                                         <  1:140928/150‑1 (MQ=255)     tttGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGc                                                                                                                                        >  2:547452/1‑151 (MQ=255)            aTTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTa                                                                                                                                   >  2:225544/1‑149 (MQ=255)                ggcccttttttttCTGCTTTTTTTTATTTCATGCAATTTTCTTGCTGCGCAAGCTTTTTCC‑AA‑AACAGG‑TAAGATGATTTTTTTGTCGTTTAATGCCTTAAAAACTTGCATGACCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTg                                                                                                                              <  1:254783/143‑1 (MQ=255)                 gTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGAc                                                                                                                            >  1:493033/1‑151 (MQ=255)                     aCTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACtttt                                                                                                                        >  1:130004/1‑151 (MQ=255)                     aCTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACtttt                                                                                                                        >  1:377432/1‑151 (MQ=255)                        ttttttTGCTTTTTTTTTTTTCATACATTTTTTTTGCTCCG‑AAGGTTTTTCCAAA‑AACAGT‑TAAGATAATTTTTTTTTCGCTTAATCCTTGAAAAACATGCATGAGCAAAAAAATAAAAAAAAAAACCCCGCCATTAAGTTGACTTTTAg                                                                                                                      <  1:796128/150‑1 (MQ=255)                          tttCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAgcgc                                                                                                                   >  1:601862/1‑151 (MQ=255)                               gctgttttttATTTCATAAATTCTTCCTGC‑GCCCCAGTCTTTTTC‑AA‑AAAAGGTTTAGATTATTTTTTTGTCGTTTATTCCTTTTAAAACATCCTTGCCCCACAAAAAAATAAAAAAATTCCCGCCATTAAGTTGACTTTTAGCGCCCa                                                                                                                <  1:749355/144‑1 (MQ=255)                                 tCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATAtc                                                                                                            >  2:9821/1‑151 (MQ=255)                                    tttttATTTCATGCAATTTTCTTGCGGCGCAAGCTTTTCCC‑AA‑AACAGT‑TTAAATGTTTTTTTTGTCGTTTAATGCCTGAAAAACATGCATGACCCACAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGccc                                                                                                                 <  2:302034/143‑1 (MQ=255)                                    tttttATTTCATGAAATCTTCTTGCTGCGCAAGCGTTTTCC‑AG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAACACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTcc                                                                                                         >  1:801072/1‑151 (MQ=255)                                       ttATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTcc                                                                                                         >  2:676267/1‑148 (MQ=255)                                                          tgctgcGAAAGCTTTTTCA‑AA‑AACGGG‑TTAGATGTTTTTTTTGTCGCTTAATCCCTAAAAAACATGAATGACCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCa                                                                                      <  2:531384/148‑1 (MQ=255)                                                            ctgcGCAAGCGTTTTCC‑AG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGaaa                                                                                  >  2:183622/1‑150 (MQ=255)                                                                gcAAGCGTTTTCC‑AG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtcgt                                                                             >  2:35539/1‑151 (MQ=255)                                                                gaaggctttttCA‑AA‑AACATT‑TTAGATTTTTTTTTTGTCGTTTATTCCCTGAAAAACTGGCAGGAGCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAAtt                                                                                <  1:761585/141‑1 (MQ=255)                                                                   aagtttttCCAAG‑AACAGG‑TTAGATGATTTTTTTGTCGCTTAATGCCTGAAAAACATGCATGAGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtcgtcg                                                                           <  2:759977/147‑1 (MQ=255)                                                                   aagtttttCC‑AAAAACAGG‑TTAGTTGTTTTTTTTGCCGCTAAATGCTTAAAAAACATGCAGGACCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGc                                                                                        <  2:229410/134‑1 (MQ=255)                                                                                 aaaaGG‑TTAGATGTTTTTTTTGTCGTTAAATGCCGTTAAAACATGCATGAGCCAAAAAATAATAAAAAAATTCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCa                                                                    <  2:202873/142‑1 (MQ=255)                                                                                  aCAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGc                                                             >  2:147964/1‑151 (MQ=255)                                                                                        ttAGATTTTTTTTTTGTCGTTTAATCCCTAAAAAACATGCAGGACCCAAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTg                                                         <  1:762347/150‑1 (MQ=255)                                                                                             taatttttttGTCGCTAAATGCCTGAAAAACATGCATGAGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGc                                                             <  2:377463/136‑1 (MQ=255)                                                                                                   ttttttCGTTTAATGCCTAAAAAACATGAATGACCCAAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGtcat                                              <  1:304377/150‑1 (MQ=255)                                                                                                        tCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATtgt                                        >  1:387991/1‑151 (MQ=255)                                                                                                          gCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATtgtg                                       >  1:350923/1‑150 (MQ=255)                                                                                                              aaTGCCTGAAAAACATGCATGAGCCAAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAAt                                    <  2:254521/149‑1 (MQ=255)                                                                                                                              gcaagtgCCAAAAAATAATAAAAAAATGACCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGATATTCGTCAGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagcg                  <  1:568236/145‑3 (MQ=255)                                                                                                                                aggaccaaaaaaaaaATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATaaa                     <  2:466496/137‑1 (MQ=255)                                                                                                                                   aGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagtgagtg              >  1:745475/1‑150 (MQ=255)                                                                                                                                     caaaaaaaTAAAAAAAAAATTCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagtgagt               <  2:643269/143‑1 (MQ=255)                                                                                                                                       aaaaaaTAAAAAAAAAATCCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAata          <  1:589660/148‑1 (MQ=255)                                                                                                                                         aaaaaaaaaaaaaaaaCCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGTATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAat           <  1:734993/147‑1 (MQ=255)                                                                                                                                         aaaaaaaaaaaaaaACCCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATtc       <  1:10467/151‑1 (MQ=255)                                                                                                                                           aaaaataTAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATtctc     <  2:118039/148‑1 (MQ=255)                                                                                                                                              aataTAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTgg  >  2:20953/1‑151 (MQ=255)                                                                                                                                                  |                                                                                                                                                   AAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGG  >  NC_000913/29354‑29642

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑