Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,378,796	0	T	A	48.8%	35.4 / 24.8	41	Y50F (TAT→TTT)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
Reads supporting (aligned to +/- strand):  ref base T (12/9);  new base A (0/20);  total (12/29)
Fisher's exact test for biased strand distribution p-value = 5.32e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATTTCCCCTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGT‑GTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑TT‑ACCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGT  >  NC_000913/4378648‑4378932                                                                                                                                                       |                                                                                                                                            gATTTCCCCTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGT‑GTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATa                                                                                                                                            <  2:723310/150‑1 (MQ=255)     tCCCCTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGT‑GTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑tt                                                                                                                                       <  1:431225/150‑1 (MQ=255)       cccTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGT‑GTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑TT‑acc                                                                                                                                   >  2:1156245/1‑151 (MQ=255)        ccTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGT‑GTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑TT‑accg                                                                                                                                  <  2:272880/151‑1 (MQ=255)           cGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGT‑GTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑TT‑accgcc‑a                                                                                                                              <  1:1083384/151‑1 (MQ=255)              gCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGT‑GTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑TT‑accgcc‑accg                                                                                                                           <  1:462170/151‑1 (MQ=255)               cAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGT‑GTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑TT‑accgcc‑accgc                                                                                                                          >  1:349628/1‑151 (MQ=255)                aaTAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGT‑GTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑TT‑accgcc‑accgcc                                                                                                                         >  1:1180920/1‑151 (MQ=255)                               aaGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGT‑GTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑TT‑ACCGCC‑ACCGCCATACCCGGGATCttt                                                                                                          >  2:918906/1‑151 (MQ=255)                               aaGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGT‑GTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑TT‑ACCGCC‑ACCGCCATACCCGGGATCttt                                                                                                          >  2:1108630/1‑151 (MQ=255)                                    ccccAGTAATTTTTTTGCTGACCGACCCAAACAAAAACAATTTTTGTTGT‑GGGGGGGGTTTTTTTTTGGGGATGCCCGAACCCCCCCAGATAAAGAAATAGGTTTTCCCC‑TAAAAAA‑TT‑CCCCCC‑ACCGCCATACCCGGGATCTTttgttg                                                                                                     <  2:873460/149‑1 (MQ=255)                                    cGCCAGTAATTTTTTTGCTGCCCG‑ACCCAACCCAAACAACCTTTTTTTTGGTGAGGGGTTTTTTTTGGGCGTTGCCCGCATCCCCCCGGTAAAAGAAATAGTTTTTCCCC‑TAAAAAT‑TC‑CCCGCC‑ACCGCCATACCCGGGATCTTttgt                                                                                                       <  2:1060128/149‑1 (MQ=255)                                    cGCCAGTAAATTTTTTGCTGACCGACCCTAACAAAAACACCGTTTGTTGT‑GTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAATAAATAGGGTTTCCCC‑TGAAAAA‑TA‑CCCGCC‑ACCGCCATGCCCGGGATCTTttgttg                                                                                                     <  1:62016/151‑1 (MQ=255)                                      ccAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGT‑GTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑TT‑ACCGCC‑ACCGCCATACCCGGGATCTTTTGTTGct                                                                                                   >  2:1011951/1‑151 (MQ=255)                                           aatttttttGGTGCCCGACCCTAACCAAAACACCTTTTGTTGG‑GGGACGGGCTGTTTTTTGGCGTTGTCCGAAT‑GCCCCAGGGAAAATTAAAAAGTTTGCCC‑TGAAAAA‑TTCCCCCCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCtata                                                                                              <  1:641700/146‑1 (MQ=255)                                                  ttGCTGCCCGAACCTAACTAAAACAACTTTTGTTGT‑GTGGGGGGCTGTTTTTTGGCGATGTCCGCATACCCCCAGGAAAATTAATAAGTTTTCCCT‑TAATAAT‑TT‑CCCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCggg                                                                                        <  1:854313/150‑1 (MQ=255)                                                       gACCGAACCTAACTCAAACAACGTTTGCTGT‑GTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑TT‑ACCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAAtt                                                                                  >  2:596596/1‑151 (MQ=255)                                                              caaaacaaaaaCAAGTTTGGCTGT‑GTGCGGGGTTTTTTTTGGGCGATGCCCCCATCCCCCCAGAAAAATTAATAAGTTTTCCCC‑TAAAAAT‑TC‑CCCCCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGa                                                                            <  2:277068/142‑1 (MQ=255)                                                                      aaaCACCTTTTGCGGT‑GTGGCGGGTTGTTTTTGGGCGATGCCCGCATACCCCCAGAAAAAGTAATAGGTTTTCCCT‑TAAAAAA‑TT‑CCCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGc                                                                         <  1:347765/145‑1 (MQ=255)                                                                       aacaccTTTTGCTGT‑GTGGGGGGTTTTTTTTTGGCGATGCCCGAATAGCCCAAGGAAAATTAATAAGTTTTCCCG‑TAATAAT‑TT‑CCCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAatat                                                                  <  1:349534/151‑1 (MQ=255)                                                                         caacGTTTGCTGT‑GTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑TT‑ACCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCg                                                                >  2:903709/1‑151 (MQ=255)                                                                         aaacGTTGGTTGT‑GGGACGGGTTTTTTTTGGGCGATGCCCGCATACCCCGAGAAAAAGTAATAGGTTTTCCCC‑TAAAAAA‑TC‑CCCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCg                                                                <  1:226902/150‑1 (MQ=255)                                                                                    gt‑gtgACGGGCTGTTTTTGGGCGTTGCCCGCATACCCCAAGGTAAAAAAATAAGGTTTCCCC‑TAAAAAT‑TT‑CCCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATttgtt                                                      <  1:248830/150‑1 (MQ=255)                                                                                     t‑gtgACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑TT‑ACCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATttgtt                                                      >  2:212622/1‑149 (MQ=255)                                                                                         gaggggCTGTTTTTTGGCGATCCCCGCATACCCCAGGGTAAAGAAATAAGTTTTCCCT‑TAAAAAA‑TT‑CCCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAgg                                                  <  1:467251/147‑1 (MQ=255)                                                                                           ggggTTGTTTTTTGGCGATCCCCCCAT‑CCCCCAAGAAAAAAAAAAAGGTTTTCCCTTAAAAAA‑TC‑CCCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAgggg                                                <  2:898020/149‑1 (MQ=255)                                                                                            gggTTGTTTTTGGGCGATGCCCGCAAACCCCCAGGAAAAGTAAAAAGTTTTACCT‑TAAAAAA‑TT‑CCCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATttg                                                        <  1:549195/141‑1 (MQ=255)                                                                                                   tttttGGCGATGCCCGCATAGCCCAAGGAAAAGTAATAAGTTTTCCCT‑TAAAAAA‑TT‑CCCCCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAAt                                        <  1:127577/150‑1 (MQ=255)                                                                                                          gcatacctgcaccgCCCCAGTAAAAAGAATAAGG‑TTCGCT‑TGATGAA‑AT‑ACCGCCGGCCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAg                                  <  1:1156255/136‑1 (MQ=255)                                                                                                                ccGCATCCCCCCAGGAAAAATAAAAAGTTTTACCA‑TAAAAAA‑TT‑CCCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAagag                            <  1:1101693/149‑1 (MQ=255)                                                                                                                      aGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑TT‑ACCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGtaa                     >  2:612518/1‑150 (MQ=255)                                                                                                                        cccagggaaaaGAAAAAAGGTTTCCCT‑TAAAAAA‑TC‑CCCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGtaat                    <  1:1095383/141‑1 (MQ=255)                                                                                                                            aGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑TT‑ACCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATtaata               >  2:112278/1‑150 (MQ=255)                                                                                                                             ggTAAAGAAAAAAGTTTTCCCC‑TAAAAAA‑TC‑CCCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCgg                        <  1:1069250/140‑1 (MQ=255)                                                                                                                                aaaGTAAT‑AGGTTTTCCC‑ATAAAAA‑TTCCCCCCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAg             <  2:509905/148‑1 (MQ=255)                                                                                                                                aaaGTAAAAGGTTTTCCCC‑AAAAAAA‑TT‑CCCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGgcg          <  2:349626/151‑1 (MQ=255)                                                                                                                                aaaGAAAAAAGTTTTCCCT‑TAATAAT‑TT‑CCCCCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAgg            <  1:355438/149‑1 (MQ=255)                                                                                                                                 aaattaaaaGGTTTTCCC‑TTAAAAATTT‑CCCCCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAg             <  1:29208/141‑1 (MQ=255)                                                                                                                                    taataaGGTTTACCC‑TGATAAA‑TT‑ACCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGgccc         >  1:341044/1‑146 (MQ=255)                                                                                                                                      aaaaGGTTTTCCCTTGAAAAA‑TC‑CCCCCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCagag     <  1:668421/149‑1 (MQ=255)                                                                                                                                          gtttaaCCT‑TGAAAAT‑TT‑CCCCCA‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGcgt  <  1:695568/144‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                            GATTTCCCCTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGT‑GTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑TT‑ACCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGT  >  NC_000913/4378648‑4378932

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑