Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,639,030	C→T	*166* (TAG→TAA)	rzpQ ←	Rz‑like protein, Qin prophage

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,639,030	0	C	T	100.0%	60.9 / NA	20	*166* (TAG→TAA)	rzpQ	Rz‑like protein, Qin prophage
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (9/11);  total (9/11)

TGATTAAGACCTTTTATCTTACCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCCTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTGCGATGTAGCGTTCGTCAGCAATTTCAGCATAAAGCTGAGCTTCTGCTGCAATATCTCCGAGCAT  >  NC_000913/1638917‑1639152                                                                                                                  |                                                                                                                           tGATTAAGACCTTTTATCTTACCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTa                                                                                                   <  1:74313/139‑1 (MQ=255)    ttAAGACCTTTTATCTTACCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAg                                                                                                <  1:1325869/139‑1 (MQ=255)                 tCTTACCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTg                                                                                   >  1:751081/1‑139 (MQ=255)                     aCCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTa                                                                                                   <  2:564980/119‑1 (MQ=255)                     aCCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTa                                                                                                   >  1:564980/1‑119 (MQ=255)                     aCCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGa                                                                               >  1:1600918/1‑139 (MQ=255)                          tAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGt                                                                          <  2:751081/139‑1 (MQ=255)                          tAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGt                                                                          <  2:1600918/139‑1 (MQ=255)                             gATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCAc                                                                       <  1:422317/139‑1 (MQ=255)                                                 aTGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTGCGATGTAGCGTTCGt                                                   >  1:392512/1‑139 (MQ=255)                                                           ccTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTAt                                                                                                         <  1:561644/75‑1 (MQ=255)                                                           ccTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTAt                                                                                                         >  2:561644/1‑75 (MQ=255)                                                                             aCATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTg                                                                  >  1:377226/1‑96 (MQ=255)                                                                             aCATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTg                                                                  <  2:377226/96‑1 (MQ=255)                                                                                 tCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGt                                                                          <  2:157698/84‑1 (MQ=255)                                                                                 tCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGt                                                                          >  1:157698/1‑84 (MQ=255)                                                                                      gATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTGCGATGTAGCGTTCGTCAGCAATTTCAGCATAAAGCTGAGCTTCTGCTGCAat              <  2:392512/139‑1 (MQ=255)                                                                                                  ccGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTGCGATGTAGCGTTCGTCAGCAATTTCAGCATAAAGCTGAGCTTCTGCTGCAATATCTCCGa      >  1:648980/1‑135 (MQ=255)                                                                                                  ccGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTGCGATGTAGCGTTCGTCAGCAATTTCAGCATAAAGCTGAGCTTCTGCTGCAATATCTCCGa      <  2:648980/135‑1 (MQ=255)                                                                                                  ccGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTGCGATGTAGCGTTCGTCAGCAATTTCAGCATAAAGCTGAGCTTCTGCTGCAATATCTCCGAGCAt  >  1:1409990/1‑139 (MQ=255)                                                                                                                  |                                                                                                                           TGATTAAGACCTTTTATCTTACCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCCTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTGCGATGTAGCGTTCGTCAGCAATTTCAGCATAAAGCTGAGCTTCTGCTGCAATATCTCCGAGCAT  >  NC_000913/1638917‑1639152

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑