Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,378,802	0	A	C	70.6%	0.1 / 31.5	34	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
Reads supporting (aligned to +/- strand):  ref base A (9/1);  new base C (0/24);  total (9/25)
Fisher's exact test for biased strand distribution p-value = 1.91e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.04e-05

CCCTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGT‑GTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑TT‑ACCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTTGAACATA  >  NC_000913/4378654‑4378945                                                                                                                                                         |                                                                                                                                                 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)                                                                                                                                                aaaaa‑TT‑CCCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTTGAACATa  <  1:602681/149‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                                 CCCTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGT‑GTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAA‑TT‑ACCGCC‑ACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTTGAACATA  >  NC_000913/4378654‑4378945

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: ‑