Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	29,496	0	T	A	48.9%	34.8 / 37.1	47	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
Reads supporting (aligned to +/- strand):  ref base T (19/5);  new base A (0/23);  total (19/28)
Fisher's exact test for biased strand distribution p-value = 7.37e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTG‑CTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACAT‑GCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGGA  >  NC_000913/29354‑29643                                                                                                                                                   |                                                                                                                                                    aaaTTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTGTTATTTCATGCAATCTTCTTG‑CTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACAT‑GCATGAGCCACAAAATAATATAAAAAATc                                                                                                                                             <  1:723765/151‑1 (MQ=255)   aTTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTG‑CTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACAT‑GCATGAGCCACAAAATAATATAAAAAATcc                                                                                                                                            >  1:563420/1‑150 (MQ=255)    ttttGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTG‑CTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACAT‑GCATGAGCCACAAAATAATATaa                                                                                                                                                   >  2:52931/1‑142 (MQ=255)    ttttGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTG‑CTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACAT‑GCATGAGCCACAAAATAATATaa                                                                                                                                                   <  1:52927/142‑1 (MQ=255)             tttGGTCCTTTTTTTTCTGCTCTTTTTTTTTTCATGCATTTTTTTTG‑CTGCGAAAGCTTTTTCA‑AAAAAAGTTTAGATTATTTTTTTGTCGTTAAATCCT‑TAAAAAACAT‑GAATGACCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGt                                                                                                                                 <  1:340086/151‑1 (MQ=255)             tttGGCCCATTTTTTTCTGCTCTTTTTTATTTCATGCAATCTTCTTG‑CTGCGAAAGCGTTTCCC‑AGAACAGGTTAGATGATTTTTTTGTCGCTTAATGCC‑TGAAAAACAT‑GCATGAGCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGt                                                                                                                                 <  2:102214/151‑1 (MQ=255)                    cttttttttCTTCTCTTTTTTTTTTCGAGCATTCTTCTTG‑CGGCGCAGGCGTTTCCC‑AAAACGGGTTAGATGATTTTTTTGCGGCTAAATGCC‑TCAAAAACAT‑GCGTGAGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACttt                                                                                                                          <  2:790126/148‑1 (MQ=255)                                  tgTTTTTTTTTCTTGCAGTC‑TCTTGTCGGTGCTAGCGTTTCCG‑AGAATGGGTTGGATG‑TTTTTTTTTACCGTAACGGC‑TTGAAAAAATAGCTTGGGCCCAAAAAAAATATAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATAtct                                                                                                            <  1:117267/150‑1 (MQ=255)                                    tttttATTTTATGCATTTTTCTGG‑CTGCGAAAGCTTTTCCC‑AAAACGGGTAAAATGATTTTTTTGTCGTTTATTGCC‑GTAAAAACAT‑GCAGGACCCAAAAAATAATAAAAAAACCCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTcc                                                                                                          <  1:525955/151‑1 (MQ=255)                                    tttttATTTCATGCAATCTTCTTG‑CTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACAT‑GCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATAtctc                                                                                                           >  1:481638/1‑150 (MQ=255)                                         ttttCATGCATTCTTCTTG‑CTGCGCAAGTTTTTCCC‑AGAACAGGTTAGATTATTTTTTTGTCCCTTAATCCC‑TAAAAAACAT‑GCATGACCCAAAAAATAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAAt                                                                                                     <  2:489584/150‑1 (MQ=255)                                                   aTCTTCTTG‑CTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACAT‑GCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGttt                                                                                           >  2:116317/1‑151 (MQ=255)                                                    tcttctTG‑CTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACAT‑GCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTg                                                                                          >  2:44432/1‑151 (MQ=255)                                                      ttctgG‑CTCCGCAGGCTTTTCCC‑AAAAAAGGTTAAATAATTTTTTTGCCGTTAAATCCC‑TAAAAAACAG‑ACATGACCCAAAAAAAAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGcc                                                                                        <  2:399764/151‑1 (MQ=255)                                                                aaccccttttttCCAAGAAGGGGTTAAATGATTTTTTTG‑CGCTTACTTCCATAAAAAACAT‑GAATGACCAAAAAAAAAATAAAAAAATTCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtc                                                                                <  1:638171/143‑1 (MQ=255)                                                                       gTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACAT‑GCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTaa                                                                        >  1:381083/1‑151 (MQ=255)                                                                          ttCC‑AGAACCGGCTATATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACAT‑GCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATCCGTCGGTAAGCa                                                                     >  1:658174/1‑151 (MQ=255)                                                                          ttCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACAT‑GCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCa                                                                     >  1:42719/1‑151 (MQ=255)                                                                          ttCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACAT‑GCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCa                                                                     >  1:634361/1‑151 (MQ=255)                                                                                 aacggtttAGATGCTCTTTTTGTTGTTAATTGCT‑ATTAAAACAT‑GAATGACCCCAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGGCTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTg                                                               <  2:629747/145‑1 (MQ=255)                                                                                     ggTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACAT‑GCATGAGGCACAAAATAATATAAAAAATACCGACATTAAGATGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCAtt                                                           >  1:68084/1‑151 (MQ=255)                                                                                     ggTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACAT‑GCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCAtt                                                           >  1:457619/1‑151 (MQ=255)                                                                                         aGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACAT‑GCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGAtt                                                       >  1:725333/1‑151 (MQ=255)                                                                                          gatgatCTTTTTGTCGCTTAATGCC‑TGTAAAACAT‑GCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGAttt                                                      >  2:127959/1‑151 (MQ=255)                                                                                           atgttttttttGTCGTTTAATTCG‑TGTAAACCAT‑GAATGACCAAAAAAATATAAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCATAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGAtt                                                       <  1:721657/143‑1 (MQ=255)                                                                                            tgatTTTTTTGTCTTTTAATCCC‑TGAAAAACAT‑ACATGACCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTAc                                                    <  1:185766/151‑1 (MQ=255)                                                                                              ttttttttGTCTTTAAATGCC‑TGAAAAACTT‑GCATGAGCCAAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGt                                                  <  1:119186/148‑1 (MQ=255)                                                                                                    ttGTCTCTAAATGCC‑TAAAAAACAT‑GAATGAGCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTcatcat                                            <  1:680171/151‑1 (MQ=255)                                                                                                      ttCGCTTAATGCC‑GAAAAAACTG‑GCATGACCCAAAAAAAAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATtg                                          <  1:394479/150‑1 (MQ=255)                                                                                                          cTTAATGCC‑TGTAAAACAT‑GCATGAGCCAAAAAATAATATAAAAAATCCCGACATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGCCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGaa                                      >  2:685138/1‑151 (MQ=255)                                                                                                           taaaTGCT‑TGAAAAACAT‑GCAGGACCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAAt                                     <  2:367874/149‑1 (MQ=255)                                                                                                                  c‑TGTAAAACAT‑GCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATg                              >  1:52438/1‑151 (MQ=255)                                                                                                                     gTAAAACAT‑GCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCa                            >  1:164132/1‑151 (MQ=255)                                                                                                                        aaaCAT‑GCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAAt                         >  1:257659/1‑151 (MQ=255)                                                                                                                            at‑gcatgACCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAag                     <  2:242657/151‑1 (MQ=255)                                                                                                                             ttccttgcgCCAAAAAATAAAAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAag                     <  1:68171/143‑1 (MQ=255)                                                                                                                             attcatgACCCACAAAAAAATAAAAAAACCCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAag                     <  1:789970/148‑1 (MQ=255)                                                                                                                              tgtaagAGCAAAAAAGTAATAAAAAAAACCCCGCCATTAAGTTGACTTGTAGCGCCAATATCTCCAGAATGCCGCCGTTTGCCAGAAAGTCGTCGGTAAACAGATTTGCATTTATTTACGTCATCAGTGTGAATTAATATGAAAATAAag                     <  1:156812/145‑1 (MQ=255)                                                                                                                              taaatgAACCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAag                     <  1:458733/147‑1 (MQ=255)                                                                                                                               tagtgAGCCAAAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagtg                   <  1:384965/148‑1 (MQ=255)                                                                                                                                      ccACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAat            >  2:312743/1‑151 (MQ=255)                                                                                                                                         caAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATAtt         >  1:452034/1‑151 (MQ=255)                                                                                                                                          aaaaaaATAAAAAAAAGCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATtc        <  1:493770/151‑1 (MQ=255)                                                                                                                                          aaaaTAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATtc        <  2:129869/151‑1 (MQ=255)                                                                                                                                          aaaaTAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATtc        <  2:77781/151‑1 (MQ=255)                                                                                                                                               aataAAAAAAACTCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTgg   <  1:344997/151‑1 (MQ=255)                                                                                                                                               aataAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTgg   <  2:248241/151‑1 (MQ=255)                                                                                                                                                atatAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGGa  >  2:42996/1‑151 (MQ=255)                                                                                                                                                   |                                                                                                                                                    AAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTG‑CTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACAT‑GCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGGA  >  NC_000913/29354‑29643

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑