Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,103,871	(A)7→6	intergenic (+71/+78)	BW25113_RS15410 → / ← yghD	tRNA‑Phe/GspM family type II secretion system protein YghD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,103,865	0	A	.	100.0%	318.9 / NA	71	intergenic (+65/+84)	BW25113_RS15410/yghD	tRNA‑Phe/GspM family type II secretion system protein YghD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (25/46);  total (25/46)

GATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTT  >  NZ_CP009273/3103781‑3103950                                                                                     |                                                                                      gATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGaaaaaa                                                                                  >  1:2391484/1‑90 (MQ=255) gATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGaaaaaa                                                                                  >  1:1888955/1‑90 (MQ=255) gATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGaaaaaa                                                                                  >  1:1578037/1‑90 (MQ=255)  aTTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGaaaaaat                                                                                 <  1:2587051/90‑2 (MQ=255)  aTTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGaaaaaat                                                                                 >  1:1804763/1‑89 (MQ=255)     ccGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGaaaaaattag                                                                              >  1:1667489/1‑86 (MQ=255)      cGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGc                                                                            <  1:1245449/90‑1 (MQ=255)       gAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCt                                                                           >  1:1039341/1‑90 (MQ=255)       gAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCt                                                                           >  1:802552/1‑90 (MQ=255)           ccGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTtata                                                                       <  2:1692963/90‑1 (MQ=255)           ccGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTtata                                                                       >  2:819743/1‑90 (MQ=255)           ccGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTtata                                                                       <  1:2103602/90‑1 (MQ=255)            cGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATaa                                                                      <  1:1733465/90‑1 (MQ=255)            cGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATaa                                                                      >  2:1344380/1‑90 (MQ=255)            cGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATaa                                                                      <  1:653762/90‑1 (MQ=255)            cGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATaa                                                                      <  1:487819/90‑1 (MQ=255)            cGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCGGACAATAACCTTCACG‑AAAAAATTAGCTTATaa                                                                      <  1:1638190/90‑1 (MQ=255)             gggCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATaaa                                                                     >  1:2914838/1‑90 (MQ=255)             gggCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATaaa                                                                     >  1:1238745/1‑90 (MQ=255)                 accacTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCt                                                                 <  1:2774576/90‑1 (MQ=255)                  ccacTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTg                                                                >  1:2885933/1‑90 (MQ=255)                    acTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTggg                                                              <  2:941739/90‑1 (MQ=255)                    acTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTggg                                                              >  1:2383973/1‑90 (MQ=255)                            ttAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTAc                                                      >  1:151351/1‑90 (MQ=255)                            ttAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTAc                                                      <  2:151351/90‑1 (MQ=255)                              aaGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTActc                                                    <  2:708832/90‑1 (MQ=255)                               aGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTActct                                                   >  2:1444361/1‑90 (MQ=255)                                 aaCCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATaa                                                                      >  2:79178/1‑69 (MQ=255)                                 aaCCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATaa                                                                      <  1:79178/69‑1 (MQ=255)                                  aCCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGc                                                <  1:2119386/90‑1 (MQ=255)                                  aCCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGc                                                <  2:1728883/90‑1 (MQ=255)                                  aCCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGc                                                <  2:2222018/90‑1 (MQ=255)                                   cccGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGcc                                               >  1:2548606/1‑90 (MQ=255)                                    ccGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCa                                              <  2:1578037/90‑1 (MQ=255)                                     cGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCt                                                                           >  1:2758642/1‑60 (MQ=255)                                     cGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCt                                                                           <  2:2758642/60‑1 (MQ=255)                                     cGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCAc                                             >  2:1312070/1‑90 (MQ=255)                                     cGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCAc                                             >  1:2104489/1‑90 (MQ=255)                                     cGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCAc                                             >  1:2838203/1‑90 (MQ=255)                                           caAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCT‑GGGGAATTACTCTCGCCACGTTAACg                                      <  2:2687323/90‑1 (MQ=255)                                            aaGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACg                                      <  1:594344/90‑1 (MQ=255)                                            aaGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACg                                      <  1:517830/90‑1 (MQ=255)                                            aaGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACg                                      <  1:431957/90‑1 (MQ=255)                                            aaGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACg                                      <  2:2914838/90‑1 (MQ=255)                                            aaGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACg                                      <  1:2663741/90‑1 (MQ=255)                                             aGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACga                                     >  2:2500661/1‑90 (MQ=255)                                             aGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACga                                     >  1:1081635/1‑90 (MQ=255)                                               gCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACgaga                                   <  1:506135/90‑1 (MQ=255)                                                 gggTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGt                                 <  2:1410551/90‑1 (MQ=255)                                                 gggTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGt                                 >  1:2817775/1‑90 (MQ=255)                                                 gggTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGt                                 <  2:1081635/90‑1 (MQ=255)                                                         gCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTAt                         <  1:729227/90‑1 (MQ=255)                                                          tttttGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTGCTCTCGCCCCGTTATCGAGAGTAATTTTAtt                        <  1:2038033/89‑1 (MQ=255)                                                          cTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTAtt                        <  2:2111305/90‑1 (MQ=255)                                                          cTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTAtt                        <  2:2383973/90‑1 (MQ=255)                                                          cTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTAtt                        <  2:2817775/90‑1 (MQ=255)                                                          cTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTAtt                        <  1:2603655/90‑1 (MQ=255)                                                          cTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTAtt                        <  2:1238745/90‑1 (MQ=255)                                                                   cTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAt               <  2:359842/90‑1 (MQ=255)                                                                   cTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAt               <  2:566151/90‑1 (MQ=255)                                                                   cTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAt               <  2:2352499/90‑1 (MQ=255)                                                                   cTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAt               <  1:1824435/90‑1 (MQ=255)                                                                         aTAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTg         >  2:2720140/1‑90 (MQ=255)                                                                           aaCCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGAt       <  1:721510/90‑1 (MQ=255)                                                                           aaCCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGAt       <  2:2741857/90‑1 (MQ=255)                                                                           aaCCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGAt       <  2:2185694/90‑1 (MQ=255)                                                                           aaCCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGAt       <  2:1804763/90‑1 (MQ=255)                                                                           aaCCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGAt       <  1:1524890/90‑1 (MQ=255)                                                                           aaCCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGAt       <  2:1507736/90‑1 (MQ=255)                                                                           aaCCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATAATAATCTCCTGAt       <  2:2838203/90‑1 (MQ=255)                                                                               ttCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGc                                                <  1:2931309/45‑1 (MQ=255)                                                                               ttCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGc                                                >  2:2931309/1‑45 (MQ=255)                                                                               ttCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACtt   >  1:2058955/1‑90 (MQ=255)                                                                               ttCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACtt   >  2:2455939/1‑90 (MQ=255)                                                                               ttCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACtt   >  1:2243364/1‑90 (MQ=255)                                                                               ttCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTCAACGAGAGTAATTTTATTGATATTAATCTCCTGATACtt   >  1:2280451/1‑90 (MQ=255)                                                                                tCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACttt  <  2:122533/90‑1 (MQ=255)                                                                                     |                                                                                      GATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTT  >  NZ_CP009273/3103781‑3103950

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑