Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	29,496	0	T	A	50.0%	25.5 / 30.0	36	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
Reads supporting (aligned to +/- strand):  ref base T (17/1);  new base A (0/18);  total (17/19)
Fisher's exact test for biased strand distribution p-value = 4.19e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTT‑CCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGT‑AAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCT  >  NC_000913/29346‑29638                                                                                                                                                         |                                                                                                                                               tttAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTT‑CCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGT‑AAAACATGCATGAGCCACAAAATAatat                                                                                                                                                <  1:477853/151‑1 (MQ=255)          aaTTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTT‑CCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGT‑AAAACATGCATGAGCCACAAAATAATATAAAAAATc                                                                                                                                        >  1:233403/1‑150 (MQ=255)                      ttGGTCCTTTTTTTTCTGCTCTTTTTTTTTTCATGAAATCTTCTTGCTGCGAAAGCTTTTT‑CCAGAACAGGTTAGATAATTTTTTTGCCGTTAAATGCCTAA‑AAAACATGCATGACCCAAAAAATAATAAAAAAAATCCCGCCATTAAGtt                                                                                                                           <  1:638691/151‑1 (MQ=255)                             aCTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTT‑CCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGT‑AAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACtttt                                                                                                                    >  2:418680/1‑151 (MQ=255)                                         tttttttttttTCATGAATTTTTTTTGCTGCGAAAGCTTTTC‑CCAGAACGGGTTAGATATTTTTTTTGTCGCTAAATGCCTAA‑AAAACATGCAGGCCCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATAtc                                                                                                        <  2:374622/148‑1 (MQ=255)                                         cctttttttttTAATGAATTCTTCTTGCGCCACAGGTTTTTC‑CAAAAAAAGTTTAAATAATTTTTTTGTCCCTTAATGCCGTA‑AAAACATGCAGGACCCAAAAAATAATAAAAAAATTCCCGCCATTAAGTTGACTTTTAGCGCCCATAtc                                                                                                        <  2:199461/148‑1 (MQ=255)                                            ttttttttTCATGCATTTTTTTTGCTGCCAAGGCTTTTC‑CCAAAACAGTTTAGATATTTTTTTTGTCCTTTAATGCCTAA‑AAAACGTGCATGACACAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTcc                                                                                                     <  1:594172/151‑1 (MQ=255)                                            tttttATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTT‑CCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGT‑AAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATAtctc                                                                                                      >  2:633127/1‑150 (MQ=255)                                            tttttATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTT‑CCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGT‑AAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATAtctc                                                                                                      >  2:475317/1‑150 (MQ=255)                                              tttATTCAATGCATTCTTTTTGTGGCGCAGGCTTTTT‑CAAGAACAGTTTAGATAATTTTTTTTTCGCTAAATGCCTAA‑AAAACTTGCATGACCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAg                                                                                                   <  1:122788/151‑1 (MQ=255)                                                tATTTCATACATTCTTCTTGCTCCG‑AAGTGTTTTCCCAGAAAAGGTTAAATAATTTTTGTGTCCCTAAAGCCATAA‑AAAACATGCAGAAGCAAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGaa                                                                                                 <  1:423203/151‑1 (MQ=255)                                                           aTCTTCTTGCTGCGCAAGCGTTTT‑CCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGT‑AAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGttt                                                                                      >  2:578700/1‑151 (MQ=255)                                                           aTCTTCTTGCTGCGCAAGCGTTTT‑CCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGT‑AAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGttt                                                                                      >  1:284955/1‑151 (MQ=255)                                                               tcttGCTGCGCAAGCGTTTT‑CCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGT‑AAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCa                                                                                  >  2:96444/1‑151 (MQ=255)                                                                    ctgcGCAAGCGTTTT‑CCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGT‑AAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAAt                                                                             >  2:88774/1‑151 (MQ=255)                                                                      gcgcAAGCGTTTT‑CCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGT‑AAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAAtt                                                                            >  1:109252/1‑150 (MQ=255)                                                                            gCGTTTT‑CCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGT‑AAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGt                                                                     >  1:147459/1‑151 (MQ=255)                                                                                 tt‑CCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGT‑AAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCa                                                                >  2:77724/1‑151 (MQ=255)                                                                                    ccAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGT‑AAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGa                                                              >  1:135032/1‑151 (MQ=255)                                                                                    ccAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGT‑AAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGa                                                              >  1:521217/1‑151 (MQ=255)                                                                                            gttaaaatagtttttttGTC‑CTTAAATCCTGTAAAAACAGGCAAGCCCCAAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCAt                                                       <  2:548774/138‑1 (MQ=255)                                                                                            ggTTAGATGATCTTTTTGTCGCTTAATGCCTGT‑AAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCAtt                                                      >  2:472553/1‑151 (MQ=255)                                                                                            ggTTAGATGATCTTTTTGTCGCTTAATGCCTGT‑AAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCAt                                                       >  1:548603/1‑150 (MQ=255)                                                                                                  ataatttttttGTCGATAATTGCCTGA‑AAAACGTGCTTGACACAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGAtt                                                  <  1:463323/143‑1 (MQ=255)                                                                                                             tccttttAAGGCTTGA‑AAAACAGACATGAGCAAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATtg                                     <  1:280723/146‑1 (MQ=255)                                                                                                                  ttAAAGCCTTT‑AAAACCTTAAGGGGCCAAAAAATAAATAAAAAAAACCCTCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATTCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTGCGTCATCATTGTGAAt                                <  2:202340/151‑1 (MQ=255)                                                                                                                        cccgtaaaaaCATGCAGGGCCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAata                           <  2:307634/145‑1 (MQ=255)                                                                                                                           tgaaaaaCTTGAATGACCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGc                        <  2:317538/148‑1 (MQ=255)                                                                                                                                 aCATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATaa                  >  2:85132/1‑151 (MQ=255)                                                                                                                                   tgggaggggCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTGGCGCCCATATCTCCAGAATGCCGCGGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAag                <  2:306619/143‑1 (MQ=255)                                                                                                                                   atgcttgccccAAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAag                <  2:301912/142‑1 (MQ=255)                                                                                                                                   atgcatgACCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAag                <  1:90368/151‑1 (MQ=255)                                                                                                                                   atactggaacaaaaaaaTAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAag                <  1:620061/138‑1 (MQ=255)                                                                                                                                    tgcatgAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagt               >  1:587388/1‑151 (MQ=255)                                                                                                                                     acttgAGCAAAAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAag                <  1:587914/146‑1 (MQ=255)                                                                                                                                      aatgACCCAAAAAATAAAAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagtg              <  1:88762/149‑1 (MQ=255)                                                                                                                                                 aaaaaaTAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATtct  <  2:53014/151‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                               TTTAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTT‑CCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGT‑AAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCT  >  NC_000913/29346‑29638

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑