Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,378,802	0	A	C	57.6%	36.3 / 51.1	33	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
Reads supporting (aligned to +/- strand):  ref base A (14/0);  new base C (0/19);  total (14/19)
Fisher's exact test for biased strand distribution p-value = 1.22e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-08

AATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTT‑GGCGATGTCCGCATAGCCCCAG‑GTAAAGTAATAAGG‑TTT‑ACCCTG‑ATAAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTTGAACAT  >  NC_000913/4378663‑4378944                                                                                                                                                  |                                                                                                                                               aaTAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTT‑GGCGATGTCCGCATAGCCCCAG‑GTAAAGTAATAAGG‑TTT‑ACCCTG‑ATAAATT‑accgccaccgcc                                                                                                                                     <  1:700521/151‑1 (MQ=255)   tAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTT‑GGCGATGTCCGCATAGCCCCAG‑GTAAAGTAATAAGG‑TTT‑ACCCTG‑ATAAATT‑ACCGCCACCGCCAt                                                                                                                                   >  1:175947/1‑151 (MQ=255)    aGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTT‑GGCGATGTCCGCATAGCCCCAG‑GTAAAGTAATAAGG‑TTT‑ACCCTG‑ATAAATT‑ACCGCCACCGCCAt                                                                                                                                   >  1:297651/1‑150 (MQ=255)              ccaAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTT‑GGCGATGTCCGCATAGCCCCAG‑GTAAAGTAATAAGG‑TTT‑ACCCTG‑ATAAATT‑ACCGCCACCGCCATACCCGGGATCt                                                                                                                        >  2:49820/1‑151 (MQ=255)                             atttttttGCTGACCAACCATAACTCAAACAACTTTGGTTGTGTGAGGGGCTGTTTTTT‑GGAGTTGCCCGCTCACCCCAGG‑GTAAATTAA‑AAAG‑TTT‑TCCTCG‑AAAAATTCCCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATaa                                                                                                         <  1:128427/147‑1 (MQ=255)                             aaTGTTTTGCTGACCAAACCAAACCCAAACATTGTTTGGTGTGGGAGGGGTTGTTTTTT‑GGCATTGTCCGCAT‑CCCCCAGAAAAAAGAAATAAGT‑TTT‑ACCCAA‑ATAATTC‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATaa                                                                                                         <  2:488111/151‑1 (MQ=255)                               ttttttGCGGACCAAACCAAACTAAAACAAGTTTTGTTGTGTGAGGGGTTGTTTTTG‑GGCGATGCCCCCATA‑CCCCAG‑GAAAAATTAAAAGGTTTT‑CCCCTA‑AAAAATT‑CCCCCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAg                                                                                                        <  2:670132/148‑1 (MQ=255)                                tttttCCTGCCCGACCCTACCCAAAACACCTTTTGTTGTGTG‑CGGGTTTTTTTTTGGGCGTTGCCCGCATCCCCCGAG‑GTAAAGAAATAAGT‑TTT‑CCCTTG‑ATAAATT‑CCCCCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAg                                                                                                        <  2:526809/148‑1 (MQ=255)                                    tcctgccaaaaCATAACTCAAACAATGTTGGTTGTGTGAGGGGTTGTTTTTG‑GGCGATGTCCGCATACCCCCAG‑GAAAAGAAAGAGGT‑TTT‑CCCTTG‑AAAAATT‑CCCCCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCgggg                                                                                                   <  1:521125/141‑1 (MQ=255)                                             acccaaacaaaaaCAACGTTTGTGGTGTGAGGGGTTTCTTTTG‑GGCGATGTCCCCATAGCCCAAG‑GAAAAGTAATAGGT‑TTT‑CCCTTA‑ATAATTC‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCGCTATAAGCGGGGTAATtgtg                                                                                           <  2:36507/139‑1 (MQ=255)                                                  accacAAACAACTTTTTCTTTGTGATGGTTTTTTTTTT‑GGCGTTCCCCGCATCCCCCAAG‑AAAAAGTAATATTT‑TTT‑CCCCTA‑AAAAATT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGAt                                                                                       <  2:2881/144‑1 (MQ=255)                                                  aaccaaaaCAACTTTGGTTGTGTGCGGGGTTTTTTTTG‑GGCGTGGCCCGCA‑AGCCCCCA‑GGAAAAAAAAAAGG‑TTT‑TCCCCGAATAATTC‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGa                                                                                        <  1:697225/142‑1 (MQ=255)                                                          caacGTTTGCTGTGTGACGGGCTGCTTTTT‑GGCGATGTCCGCATAGCCCCAG‑GTAAAGTAATAAGG‑TTT‑ACCCTG‑ATAAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCg                                                                            >  2:371388/1‑151 (MQ=255)                                                               tttttggtggggggggTTGTTTTTT‑GGCGATGCCCGCATACCCCGAG‑G‑AAAATAAAAAGG‑TTT‑TCCCCT‑AAAAATTCCCCCCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGtt                                                                          <  1:348018/135‑1 (MQ=255)                                                               tttGCTGTGTGAGGGGCTGTTTTTT‑GGCGATGCCCGCATCCCCCCAG‑GAAAAGAAAAAAGT‑TTT‑ACCCTA‑AAAAATT‑CCCCCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGa                                                                        <  1:618653/150‑1 (MQ=255)                                                                   cTGTGTGACGGGCTGCTTTTT‑GGCGATGTCCGCATAGCCCCAG‑GTAAAGTAATAAGG‑TTT‑ACCCTG‑ATAAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATttgt                                                                   >  2:516003/1‑151 (MQ=255)                                                                          aCGGGCTGCTTTTT‑GGCGATGTCCGCATAGCCCCAG‑GTAAAGTAATAAGG‑TTT‑ACCCTG‑ATAAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAgggg                                                            >  1:383008/1‑151 (MQ=255)                                                                            ggtctgttTTTT‑GGCGATGCCCGCATACCCCCAG‑GTAAAGAAATAGGT‑TTT‑CCCCTA‑AAAATTT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGgc                                                           <  1:371404/147‑1 (MQ=255)                                                                                  ctTTTT‑GGCGATGTCCGCATAGCCCCAG‑GTAAAGTAATAAGG‑TTT‑ACCCTG‑ATAAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAAt                                                    >  2:492322/1‑151 (MQ=255)                                                                                                 ccGAATACCCCAAG‑GTAAAGTAA‑AAGG‑TTTCCCCCTA‑ATAATTC‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAagag                                        <  1:573707/149‑1 (MQ=255)                                                                                                         ccccAG‑GAAAATTAATAAGT‑TTT‑CCCCTA‑AAAAATT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCgg                                    <  1:74356/145‑1 (MQ=255)                                                                                                         cccaAG‑GTAAAGTATGAGGT‑TTT‑CCCCTA‑ATAAATT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGtaatt                               <  2:764855/150‑1 (MQ=255)                                                                                                           ccAG‑GTAAAGTAATAAGG‑TTT‑ACCCTG‑ATAAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATttg                                                                    >  1:137495/1‑111 (MQ=255)                                                                                                           ccAG‑GTAAAGTAATAAGG‑TTT‑ACCCTG‑ATAAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGtaattaa                             >  2:2468/1‑150 (MQ=255)                                                                                                                  aaaGAAATAGGT‑TTT‑CCCCTA‑AAAAATT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATtaata                           <  1:307494/146‑1 (MQ=255)                                                                                                                      taataaGG‑TTT‑ACCCTG‑ATAAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGgcgc                     >  2:172272/1‑148 (MQ=255)                                                                                                                       aaaaaGT‑TTT‑CCCTTA‑ATAAATT‑CCCGCCCCCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCa                    <  1:165015/145‑1 (MQ=255)                                                                                                                          aaGG‑TTT‑ACCCTG‑ATAAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGGGCAGAGcg               >  2:356837/1‑150 (MQ=255)                                                                                                                               ttt‑CCCGTG‑ATAAATC‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGcgtcg            <  2:602183/149‑1 (MQ=255)                                                                                                                                 t‑ACCCTG‑ATAAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGtttt        >  1:205483/1‑151 (MQ=255)                                                                                                                                    ccttG‑ATAATTT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGttt         <  1:739188/145‑1 (MQ=255)                                                                                                                                        g‑ATAAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTTGAACa   >  1:526865/1‑150 (MQ=255)                                                                                                                                          aaaaaTT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTTGAAc    <  1:39736/146‑1 (MQ=255)                                                                                                                                           tAAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTTGAACAt  >  2:286179/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                               AATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTT‑GGCGATGTCCGCATAGCCCCAG‑GTAAAGTAATAAGG‑TTT‑ACCCTG‑ATAAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTTGAACAT  >  NC_000913/4378663‑4378944

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: ‑