Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	584,639	C→T	intergenic (+209/+41)	appY → / ← ompT	global transcriptional activator, DLP12 prophage/DLP12 prophage, outer membrane protease VII, outer membrane protein 3b

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	584,639	0	C	T	100.0%	167.0 / NA	48	intergenic (+209/+41)	appY/ompT	global transcriptional activator, DLP12 prophage/DLP12 prophage, outer membrane protease VII, outer membrane protein 3b
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (24/24);  total (24/24)

AACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCCCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGTTTTCTATACCTGCTCCATTTTTGCTGTAGTCTGAAG  >  NC_000913/584503‑584759                                                                                                                                         |                                                                                                                         aaCCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCg                                                                                                                        >  2:338379/1‑139 (MQ=255)                    ggTTGCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCggg                                                                                                     <  2:553264/139‑1 (MQ=255)                     gTTGCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCgggg                                                                                                    <  2:752331/139‑1 (MQ=255)                        gCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGaaa                                                                                                 >  2:536684/1‑139 (MQ=255)                                             acTATAATTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTaaaa                                                                            >  1:406582/1‑139 (MQ=255)                                             acTATAATTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTaaaa                                                                            >  2:406579/1‑139 (MQ=255)                                                 taATTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGTGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAAtgtg                                                                        <  1:74099/139‑1 (MQ=255)                                                  aaTTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATgtgt                                                                       >  1:486215/1‑139 (MQ=255)                                                      gATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACtt                                                                   <  1:406579/139‑1 (MQ=255)                                                       aTGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCggg                                                                                                     <  2:688489/104‑1 (MQ=255)                                                       aTGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCggg                                                                                                     >  1:688489/1‑104 (MQ=255)                                                       aTGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAAt                                                                           >  2:65946/1‑130 (MQ=255)                                                       aTGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAAt                                                                           <  1:65946/130‑1 (MQ=255)                                                       aTGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTa                                                                  >  1:587503/1‑139 (MQ=255)                                                       aTGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTa                                                                  >  1:490775/1‑139 (MQ=255)                                                             ttCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACca                                                            >  1:412332/1‑139 (MQ=255)                                                                     gATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTgg                                                                                       <  2:889558/104‑1 (MQ=255)                                                                     gATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTgg                                                                                       >  1:889558/1‑104 (MQ=255)                                                                                 aaCCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTtata                                        <  2:412332/139‑1 (MQ=255)                                                                                  aCCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAg                                       <  2:406582/139‑1 (MQ=255)                                                                                    cTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGtt                                     <  1:638408/139‑1 (MQ=255)                                                                                     ttCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTaaa                                                                             <  2:442062/98‑1 (MQ=255)                                                                                     ttCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTaaa                                                                             >  1:442062/1‑98 (MQ=255)                                                                                      tCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCg                                                                                     >  1:896942/1‑89 (MQ=255)                                                                                      tCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCg                                                                                     <  2:896942/89‑1 (MQ=255)                                                                                      tCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGtttt                                   >  2:826560/1‑139 (MQ=255)                                                                                      tCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGtttt                                   >  1:668741/1‑139 (MQ=255)                                                                                      tCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATGTTAGTTGGCg                                                                                     >  1:558317/1‑89 (MQ=255)                                                                                      tCTGGGTTTATTGTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTCGTTGGCg                                                                                     <  2:558317/89‑1 (MQ=255)                                                                                       cTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTAc                                                                     <  1:490105/104‑1 (MQ=255)                                                                                       cTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTAc                                                                     >  2:490105/1‑104 (MQ=255)                                                                                        tGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCg                                                                                     <  2:359888/87‑1 (MQ=255)                                                                                        tGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCg                                                                                     >  1:359888/1‑87 (MQ=255)                                                                                             ttATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGTTTTCTATAcc                            <  1:338379/139‑1 (MQ=255)                                                                                                          tAATTGTTACATTGAAATGGCTAGTTATTCCTCgggg                                                                                                                     <  2:640589/37‑1 (MQ=255)                                                                                                          tAATTGTTACATTGAAATGGCTAGTTATTCCTCgggg                                                                                                                     >  1:640589/1‑37 (MQ=255)                                                                                                          tAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCgg                                                                                                      >  1:739953/1‑52 (MQ=255)                                                                                                          tAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCgg                                                                                                      <  2:739953/52‑1 (MQ=255)                                                                                                           aaTTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCg                                                                                     >  2:569922/1‑68 (MQ=255)                                                                                                           aaTTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCg                                                                                     <  1:569922/68‑1 (MQ=255)                                                                                                            aTTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGTTTTCTATACCTGCTCCATTTTTGCt             <  2:78295/139‑1 (MQ=255)                                                                                                                       gAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGTTTTCTATACCTGCTCCATTTTTGCTGTAGTCTGAAg  <  1:826560/139‑1 (MQ=255)                                                                                                                        aaaTGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTgg                                                                                       >  2:8517/1‑53 (MQ=255)                                                                                                                        aaaTGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTgg                                                                                       <  1:8517/53‑1 (MQ=255)                                                                                                                          aTGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAg                                       >  1:796607/1‑99 (MQ=255)                                                                                                                          aTGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAg                                       <  2:796607/99‑1 (MQ=255)                                                                                                                                  ttATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGTTTTCTATACCTGCTCCATTTTTGCTGTAGTCTg     <  1:71653/125‑1 (MQ=255)                                                                                                                                  ttATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGTTTTCTATACCTGCTCCATTTTTGCTGTAGTCTg     >  2:71653/1‑125 (MQ=255)                                                                                                                                         |                                                                                                                         AACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCCCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGTTTTCTATACCTGCTCCATTTTTGCTGTAGTCTGAAG  >  NC_000913/584503‑584759

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑