Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,227,734	C→T	pseudogene (1025/1436 nt)	mdtQ ←	putative multidrug resistance outer membrane protein MdtQ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,227,734	0	C	T	100.0%	116.6 / NA	34	pseudogene (1025/1436 nt)	mdtQ	putative multidrug resistance outer membrane protein MdtQ
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (16/18);  total (16/18)

TAAGACGACCACTATCGAAAATGGGTAGCGTCAGGCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAACAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGC  >  NC_000913/2227661‑2227811                                                                          |                                                                              tAAGACGACCACTATCGAAAATGGGTAGCGTCAGGCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGc                                                                        >  2:378926/1‑81 (MQ=255)      cgacCACTATCGAAAATGGGTAGCGTCAGGCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAg                                                                   <  2:378874/81‑1 (MQ=255)      cgacCACTATCGAAAATGGGTAGCGTCAGGCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAg                                                                   <  2:378873/81‑1 (MQ=255)        acCACTATCGAAAATGGGTAGCGTCAGGCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTg                                                                 <  2:378875/81‑1 (MQ=255)         ccACTATCGAAAATGGGTAGCGTCAGGCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGc                                                                <  1:378876/81‑1 (MQ=255)           aCTATCGAAAATGGGTAGCGTCAGGCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGCaa                                                              <  2:378877/81‑1 (MQ=255)             tATCGAAAATGGGTAGCGTCAGGCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGCAACg                                                            >  2:378933/1‑81 (MQ=255)                   aaaTGGGTAGCGTCAGGCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGCAACGCATCCt                                                      >  2:378920/1‑81 (MQ=255)                     aTGGGTAGCGTCAGGCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGCAACGCATCCTGt                                                    >  1:378916/1‑81 (MQ=255)                        ggTAGCGTCAGGCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGc                                                 <  1:378878/81‑1 (MQ=255)                          tAGCGTCAGGCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAg                                               <  1:378879/81‑1 (MQ=255)                           aGCGTCAGGCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAg                                               >  1:378930/1‑80 (MQ=255)                                cAGGCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGc                                         >  1:378921/1‑81 (MQ=255)                                cAGGCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGc                                         >  2:378924/1‑81 (MQ=255)                                 aGGCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGc                                         >  2:378922/1‑80 (MQ=255)                                  ggCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCa                                       <  1:378880/81‑1 (MQ=255)                                  ggCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCa                                       <  1:378882/81‑1 (MQ=255)                                  ggCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCa                                       <  1:378881/81‑1 (MQ=255)                                        ccGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGt                                 <  2:378883/81‑1 (MQ=255)                                         cGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGtt                                <  1:378884/81‑1 (MQ=255)                                         cGTAACGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTACAGGAAGGCCATCAGGtt                                <  1:378885/81‑1 (MQ=255)                                            aaCGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGAt                             >  1:378931/1‑81 (MQ=255)                                             aCGCCCATTTGCTGCGCGGAATGACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGAt                             <  1:378886/80‑1 (MQ=255)                                                       gctgcGCGGAATGACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATaa                   >  2:378925/1‑80 (MQ=255)                                                              ggAATGACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGc           >  1:378928/1‑81 (MQ=255)                                                                aaTGACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCtt         >  2:378936/1‑81 (MQ=255)                                                                 aTGACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCttt        >  2:378929/1‑81 (MQ=255)                                                                   gACGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTg      >  2:378940/1‑81 (MQ=255)                                                                     cGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGcc    <  1:378888/81‑1 (MQ=255)                                                                     cGGAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGcc    <  1:378887/81‑1 (MQ=255)                                                                      ggAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCg   >  2:378937/1‑81 (MQ=255)                                                                      ggAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCg   <  2:378889/81‑1 (MQ=255)                                                                      ggAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCg   >  2:378927/1‑81 (MQ=255)                                                                       gAATAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGc  <  1:378890/81‑1 (MQ=255)                                                                          |                                                                              TAAGACGACCACTATCGAAAATGGGTAGCGTCAGGCCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAACAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGC  >  NC_000913/2227661‑2227811

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑