Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	481,176	Δ1 bp	100%	intergenic (‑101/‑41)	acrA ← / → acrR	multidrug efflux system/transcriptional repressor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	481,176	0	A	.	100.0%	76.3 / NA	18	intergenic (‑101/‑41)	acrA/acrR	multidrug efflux system/transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (8/10);  total (8/10)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGTTGGGCCTGTTTGTCGTCACATCCTGTTAGGGCTAAGCTGCCTGAGAGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCAAATTGGTCAATGGTCAAAAGTTAATAAACCCATTGCTGCGTTTATATTATCGTCGTGCTATGGTACATACATTCACAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTACGCGCGGTGCAATCTACTGGCATTTTAAAGACAAGTCGGATTTGTTCAGTGAGATCTGGGAACTGTCAGAATCCAATATT  >  CP009273/480981‑481426                                                                                                                                                                                                    |                                                                                                                                                                                                                                                           ttttgGGCCTGTTTGTCGTCACTTCCTGTTAGGGAGAAGCTGCCTGAGAGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATCTAAACCTCGAGTGTCCGATTTCAAATTGGTCAATGGTCAAAAGTTAATAAACCCATTGCTGCGTTTATATTATCGTCGTGCTATGGTACATACATTC‑CAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGcc                                                                                                                                                                            <  1:259247/273‑1 (MQ=255)                  gtcACATCTTGTTAGGGCTAAGATGTATGAGAGTATACGAATGTCCGTCAGGGGCGTAAACCTTCTGTTTTTGTTAATATGTAAACCTTGAGTGTCCGATTTCAAATTTGTCAATGGTCAAAAGTTAATAAACCCATTGCTGCGTTTTTATTATCGTCGTGCTATGGTACATACATTC‑CAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACAGATGGCACGAAAAGCCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCGCGAtgt                                                                                                                                                            <  2:429330/274‑1 (MQ=255)                             ttAGGGCTAAGCTGCCTGAGTGCATCAGAACGACCGCCAGATGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCAAATTGGTCAATGGTCAAAAGTTAATAAACCCATTGCTGCGTTTATATTATCGTCGTGCTATGGTACATACATTC‑CAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCt                                                                                                                                                <  1:64347/275‑1 (MQ=255)                                           ccTGAGAGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCAAATTGGTCAATGGTCAAAAGTTAATAAACCCATTGCTGCGTTTATATTATCGTCGAGCTATGGTACATACATTC‑CAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAAAAACGCGCCACCACATCCTCGATGAGGCTCTACGTCTTTTCTCAcagaag                                                                                                                                   >  1:46495/1‑274 (MQ=255)                                               agagCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCAAATTGGTCAATGGTCAAAAGTTAATAAACCCATTGCTGCGTTTATATTATCGTCGTGCTATGGTACATACATTC‑CAAat                                                                                                                                                                                                                                                       <  2:227191/154‑1 (MQ=255)                                                              ccGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCAAATTGATCAATGGTCAAAAGTTAATAAACCCATTGCTGCGTTTATATTATCGTCGTGCTATGGTACATACATTC‑CAAATGTATGTAAATATAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAAAAGCGCAAGAAACGCGCCAACAAACCCTCGAAGGAGCTCCACGTCTTTTCTCACAGCAGGGGGTCTAATCCCCCTctcg                                                                                                               >  2:9237/1‑272 (MQ=255)                                                                                                                               gtcaattgtcaaAAGTTAATAAACCCATTGCTGCGTTTATATTATCGTCGTGCTATGGTACATACATTC‑CAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGTGCGAGATTGCAACAGCAGCTGGCGTTACGCGCGGTGCAATCTACTGGCATTTTAAAGACAAGt                                              <  1:79901/275‑1 (MQ=255)                                                                                                                                             ggtactaacctcATTGTTTCGTGTATAATATCGTCGTGCCAGGGTACATACATTC‑CAAATGTATGTAAATCTAACCCCTGTAAATTCACGAACATATGGCACGAGAAACCAAACAAGAAGCTCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGTGGTATCATCCACCTCGCTTGGCGGGATTGCAAAAGCAGCTGGCGTTAAGCGCGGTTCAATCTTCTGGCATTTTAAAGACAAGTCGGATTTGTTCAGt                                <  2:46495/264‑1 (MQ=255)                                                                                                                                              ttAATAAACCCATTTCTGCGTTTATATTATCGTCGTGCTATGGTACATACATTC‑CAAATGTATGTAAATCGAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACCTCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTACGCGCGGTGCAATCTACTGGCATTTTAAAGACAAGTCGGATTTGTTCAGt                                <  1:9237/274‑1 (MQ=255)                                                                                                                                                     aCCCATTGCTGCGTTTATATTATCGTCGTGCTATGGTACATACATTC‑CAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAAcg                                                                                                                                                                                >  1:281413/1‑123 (MQ=255)                                                                                                                                                         aTTGCTGCGTTTATATTATCGTCGTGCTATGGTACATACATTC‑CAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGcc                                                                                                                                                                            <  2:281402/123‑1 (MQ=255)                                                                                                                                                                       attatCGTCGTGCTATGGTACATACATTC‑CAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTAACGTACACCTCGCTGGGCGAGATTGCAAAAACAGCTGGCGTTACGCGCGGTGCAATCTACTGGCATTTTAAAGACAAATCGGATTTGTTCAGGAAGATCTGGGAACTGTCAGaaacaaa      >  1:40417/1‑270 (MQ=255)                                                                                                                                                                            cgtcgtGCTATGGTACATACATTC‑CAAATGTATGTAAATATAACGCCTGTAAATTAAAGAACATCTGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACAAATACTCGATGTGGCTCTACGTCTGTTCTCACAGCAGGGGGTATCATCAACCGAGCTGGGCGAGCTTGCAAAAGCAGCTGGCGTTAAGCGCGGGCAAATCTACTGGCATTTTAAAAACAAGGCGGATTTGTTCAGTGAGATCTGGGAACGGTCAANATctgtacat  >  2:58936/1‑267 (MQ=255)                                                                                                                                                                                ttGCTATGGTACATACATTC‑CAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACAGATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCCAGCTCGCTAGGCGAGATTGCAAAAGCAGCTCGCGTTACGCGCGGTGCAATCTACTGGCATTTTAAAGACAAGTCTGATTTGTTCAGTGAGATCTGGGa                     <  1:58936/250‑1 (MQ=255)                                                                                                                                                                                       ggTACATACATTC‑CAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTa                                                                                  >  1:104920/1‑183 (MQ=255)                                                                                                                                                                                           catacatTC‑CAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCtttt                                                                                                                                             >  2:130391/1‑120 (MQ=255)                                                                                                                                                                                           catacatTC‑CAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTAcgcg                                                                              <  2:104919/183‑1 (MQ=255)                                                                                                                                                                                              acatTC‑CAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCAAAag                                                                                              >  2:89059/1‑164 (MQ=255)                                                                                                                                                                                                    |                                                                                                                                                                                                                                                           TGTTGGGCCTGTTTGTCGTCACATCCTGTTAGGGCTAAGCTGCCTGAGAGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCAAATTGGTCAATGGTCAAAAGTTAATAAACCCATTGCTGCGTTTATATTATCGTCGTGCTATGGTACATACATTCACAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTACGCGCGGTGCAATCTACTGGCATTTTAAAGACAAGTCGGATTTGTTCAGTGAGATCTGGGAACTGTCAGAATCCAATATT  >  CP009273/480981‑481426

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑