Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	884,346	0	C	G	47.7%	56.1 / 24.5	44	A225G (GCG→GGG)	mdfA	multidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base C (3/20);  new base G (20/1);  total (23/21)
Fisher's exact test for biased strand distribution p-value = 1.88e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑ACCGGCGAGCAGTTGAGCAGCTATGAATAT‑GGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCT  >  NC_000913/884209‑884493                                                                                                                                          |                                                                                                                                                       aTTGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCGGGGGC‑Tgggg                                                                                                                                          >  1:1073068/1‑150 (MQ=255)  ttGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGGCGGCGC‑Tggg                                                                                                                                           >  1:69615/1‑149 (MQ=255)            tctcCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCGGGCGC‑TGGGGGTTGTTTGTCt                                                                                                                               >  2:81354/1‑151 (MQ=255)             ctcCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCgcgggggc‑ggggggtcggttgtgt                                                                                                                               >  2:382929/1‑138 (MQ=255)              tcCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGGTGGCGG‑GGGGGTttgtttgttt                                                                                                                               >  2:32960/1‑147 (MQ=255)               ccTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCt                                                                                                                               <  1:855812/148‑1 (MQ=255)                 tttttCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCCGGCGG‑TGGGGTGCGTTTGTCTGcc                                                                                                                            >  2:943982/1‑149 (MQ=255)                  ttttCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGGGGGCGC‑Tgggggttggtagtgt                                                                                                                               >  2:1004517/1‑133 (MQ=255)                   tttCGGTCTCCACCGAGCCATTCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGtt                                                                                                                         <  2:709152/150‑1 (MQ=255)                     tCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGGTGGGGC‑CGGGGGTCGGTTGTTTGCCgct                                                                                                                         >  2:792006/1‑146 (MQ=255)                               aCGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATc                                                                                                            <  2:283584/151‑1 (MQ=255)                                    ccATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGGCGGGGG‑CGGGGTTCGTTTGTTTGCCGTTGGTGGGGTGGGGCGcccc                                                                                                       >  1:1029172/1‑150 (MQ=255)                                     cATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCGGGCGC‑TGGGGTTCGTTTGTCTGCCGTTGCTGGGGGGGGGCGcccc                                                                                                       >  1:489488/1‑149 (MQ=255)                                      aTGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGt                                                                                                     <  1:19526/151‑1 (MQ=255)                                                   ccACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGGGGGGGG‑CGGGGGTCGTTATTCTGCGGCTGTTGGCGGGGGTGGccccccc                                                                                                    >  2:679986/1‑135 (MQ=255)                                                        cgTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑a                                                                                  <  2:509690/151‑1 (MQ=255)                                                           ataGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑Acc                                                                                <  1:983584/150‑1 (MQ=255)                                                           ataGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑Acc                                                                                <  1:48233/150‑1 (MQ=255)                                                              ggCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑ACCGGCg                                                                            <  2:769037/151‑1 (MQ=255)                                                                  agaAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGGTGGGGG‑CGGGGGTCGGTTGGGTGCCCTTGCTGGGGGGGGGCGCCCCGCCGCCGGTTATTATCATT‑atc                                                                                >  2:380483/1‑141 (MQ=255)                                                                   gaAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGGCGGCGC‑TGGGGTGTGTTAGTCTGGCGGTGCTGGGGTGGGGGGCCCCGTCGCCGGTTTTCATCATT‑TCCcgcggg                                                                          >  2:469669/1‑146 (MQ=255)                                                                    aaaCTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCTGGCGC‑CGGGGTTTGTTATTCTTCCGCTTCTGGTGTGGGGGGCCCCCCCGCCCCTTATTATCATTAACCGGCgggggg                                                                       >  1:726301/1‑146 (MQ=255)                                                                     aaCTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCCGGGGC‑CGGGGTTTGTTTGTTTGGCGGTGGTGGGGGGGGTGGCCCCCTCGCCCGTTTTTATCATT‑TACGGCggg                                                                          >  1:686848/1‑144 (MQ=255)                                                                     aaCTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑ACCGGCGAGCAGtt                                                                     <  1:1013874/151‑1 (MQ=255)                                                                      aCTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑ACCGGCGAGCAGTTg                                                                    <  2:260682/151‑1 (MQ=255)                                                                         gTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCTGGCGC‑TGGGGGTTGTTATTCTGCCGGTGCTGGGGGGGGGTGCCCACCCGCCGGTTTTTATCATT‑ACCGGCggggaggt                                                                     >  1:701620/1‑140 (MQ=255)                                                                           cACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑ACCGGCGAGCAGTTGagca                                                                <  2:36672/150‑1 (MQ=255)                                                                            aCTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCTGGGGG‑TGGGGGTCGTTAGTCTGGCCGTGGTGGCGGGGGGGGCCCCCGCGCCGGTTTTTATCATT‑AACcgcgggggggtgaggag                                                               >  2:428096/1‑137 (MQ=255)                                                                               gAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑ACCGGCGAGCAGTTGAGCAGCTAt                                                           <  1:24457/151‑1 (MQ=255)                                                                                aaaGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCTGGGGC‑TGGGGTTCGTTTGTCTGCCGTTGCTGGCGGGGGGTGCCCCCTCGCCGGTTATCATCATT‑ACCGGCGAGGAGGTgaggag                                                               >  2:372574/1‑146 (MQ=255)                                                                                 aaGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑ACCGGCGAGCAGTTGAGCAGCTATGa                                                         <  2:864972/151‑1 (MQ=255)                                                                                   gAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑ACCGGCGAGCAGTTGAGCAGCTATGAat                                                       <  2:6702/151‑1 (MQ=255)                                                                                             gTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑ACCGGCGAGCAGTTGAGCAGCTATGAATAT‑GGCTtgct                                            <  1:605184/151‑1 (MQ=255)                                                                                              tGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCCGGCGC‑TGGGGGTTGGTTGTCTTCCGTTGGTGGGGGGGGGGGCCCCCTCGCCGGTTATTATCATT‑ATCCGCGGGCAGGTGAGCAGCTATGAATAT‑TGGTtgct                                            >  1:556609/1‑150 (MQ=255)                                                                                                  tataAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCCGGGGCGGGGGTTTCGTAGTTCTG‑CGTTTGTGGGGGGGGGAGCCCCGGCGCCGCGTTTTATCATT‑TCCGGGGGGCAGTTTAGCAGGTAAGGatattggtttttatca                                         >  1:883293/1‑138 (MQ=255)                                                                                                     aaGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCCGGGGC‑CGGGGGTTGTTTGTCTGCCCTTGCTGGCGGGGGGCGCCCCCGCGCCCAGTATTCTCCTT‑ACCCGCGGGCAGGTGAGGAGGTCTGTATATAGGTTtgctcaagcg                                      >  2:73619/1‑144 (MQ=255)                                                                                                             gCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑ACCGGCGAGCAGTTGAGCAGCTATGAATAT‑GGCTTGCTGCAAGTGCCTATTTTc                            <  1:81355/151‑1 (MQ=255)                                                                                                                gaagaaCGGCCGCTTTGTGGCGGGGGGGCTGGCGC‑TTGGGGTTGTTTTTCTGCCGTTGCTGGGGGGGGTCGCCCCCTCGCCCCTTATTATTATT‑ACCGGCGGGGCGGTGAGCAGCTCTGAATAT‑AGGTTTCTGCCAGTGCCTAttttt                            >  1:477427/1‑147 (MQ=255)                                                                                                                     aCGGCCGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑ACCGGCGAGCAGTTGAGCAGCTATGAATAT‑GGCTTGCTGCAAGTGCCTATTTTCGGGGCGtt                    <  1:1051216/151‑1 (MQ=255)                                                                                                                         ccGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑ACCGGCGAGCAGTTGAGCAGCTATGAATAT‑GGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAAtt                <  2:216998/151‑1 (MQ=255)                                                                                                                          cGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑ACCGGCGAGCAGTTGAGCAGCTATGAATAT‑GGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAAtt                <  2:931538/150‑1 (MQ=255)                                                                                                                                gtgGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑ACCGGCGAGCAGTTGAGCAGCTATGAATAT‑GGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGt          <  2:636538/150‑1 (MQ=255)                                                                                                                                     gggggCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑ACCGGCGAGCAGTTGAGCAGCTATGAATAT‑GGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTg    <  1:282202/151‑1 (MQ=255)                                                                                                                                       gggCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑ACCGGCGAGCAGTTGAGCAGCTATGAATAT‑GGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCt  >  2:109973/1‑151 (MQ=255)                                                                                                                                          |                                                                                                                                                       ATTGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGC‑TGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATT‑ACCGGCGAGCAGTTGAGCAGCTATGAATAT‑GGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCT  >  NC_000913/884209‑884493

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑