Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,110,512	(A)7→6	intergenic (+71/+78)	pheV → / ← yghD	tRNA‑Phe/putative type II secretion system M‑type protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,110,506	0	A	.	100.0%	157.3 / NA	38	intergenic (+65/+84)	pheV/yghD	tRNA‑Phe/putative type II secretion system M‑type protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (15/23);  total (15/23)

ATAGCTCAGTCGGTAGAGCAGGGGATTGAAAAT‑CCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCACCATCCCAGGCTTCTCA  >  NC_000913/3110372‑3110641                                                                                                                                        |                                                                                                                                        aTAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGACCCCGCCACCAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGaaaaa                                                                                                                                     >  1:1087440/1‑140 (MQ=25)    gCTCAGTCGGTAGAGCAGGGGATTGAAAAT‑CCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGaaaaaatta                                                                                                                                 <  2:708381/140‑4 (MQ=255)            ggTAGAGCAGGGGATTGAAAAT‑CCCCGTGTCCTTGGTTCGACTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATaa                                                                                                                        <  2:892764/140‑1 (MQ=255)                 agCAGGGGATTGAAAAT‑CCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCt                                                                                                                   <  1:969817/140‑1 (MQ=255)                   cAGGGGATTGAAAAT‑CCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTgg                                                                                                                 >  2:440468/1‑140 (MQ=255)                   cAGGGGATTGAAAAT‑CCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTgg                                                                                                                 <  2:378868/140‑1 (MQ=255)                      gggATTGAAAAT‑CCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTggggg                                                                                                              >  1:324050/1‑140 (MQ=255)                       ggATTGAAAAT‑CCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGa                                                                                                             >  1:517147/1‑140 (MQ=255)                        gATTGAAAAT‑CCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGaa                                                                                                            >  2:350584/1‑140 (MQ=255)                           tGAAAAT‑CCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTa                                                                                                         <  2:324050/140‑1 (MQ=255)                             aaaaT‑CCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTAct                                                                                                       >  2:835343/1‑140 (MQ=255)                             aaaaT‑CCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTAct                                                                                                       <  1:1208899/140‑1 (MQ=255)                              aaaT‑CCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTActc                                                                                                      <  1:1157162/140‑1 (MQ=255)                                   ccccGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGc                                                                                                  >  1:386981/1‑140 (MQ=255)                                           ccTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTaa                                                                                          <  2:481991/140‑1 (MQ=255)                                           ccTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTaa                                                                                          <  2:473073/140‑1 (MQ=255)                                                 ttCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGagag                                                                                    <  2:386981/140‑1 (MQ=255)                                                      ttCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAAtt                                                                               >  1:559960/1‑140 (MQ=255)                                                         cGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTa                                                                            <  2:637149/140‑1 (MQ=255)                                                         cGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTa                                                                            <  2:1080444/140‑1 (MQ=255)                                                          gAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTAt                                                                           <  2:509680/140‑1 (MQ=255)                                                             tCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGa                                                                        <  2:559960/140‑1 (MQ=255)                                                                           aTTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGa                                                          <  1:612750/140‑1 (MQ=255)                                                                               ttAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACt                                                      <  2:46936/140‑1 (MQ=255)                                                                                     aCCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCt                                                            >  2:210422/1‑128 (MQ=255)                                                                                     aCCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCt                                                            <  1:210422/128‑1 (MQ=255)                                                                                      cccGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTAcccc                                               <  1:350584/140‑1 (MQ=255)                                                                                       ccGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTAccccc                                              >  1:200322/1‑140 (MQ=255)                                                                                         gCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGt                                            >  2:979868/1‑140 (MQ=255)                                                                                                aGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACt                                     <  2:121190/140‑1 (MQ=255)                                                                                                      gTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGcc                               >  2:183465/1‑140 (MQ=255)                                                                                                         tttGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCt                            <  1:1101775/140‑1 (MQ=255)                                                                                                                  ggATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCa                   <  1:183465/140‑1 (MQ=255)                                                                                                                   gATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCAc                  <  1:510358/140‑1 (MQ=255)                                                                                                                        gACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCACCATcc             >  2:333517/1‑140 (MQ=255)                                                                                                                          cAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTACCGAGAGTAATTTTATTGCTATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCACCATCCCa           <  2:1087440/140‑1 (MQ=255)                                                                                                                             tAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCa                   >  1:883735/1‑129 (MQ=255)                                                                                                                             tAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCa                   <  2:883735/129‑1 (MQ=255)                                                                                                                                   tCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCGAAACTCCAGCCGCAGCACATTCACCATCCCAGGCGTCTca  >  2:1075760/1‑140 (MQ=255)                                                                                                                                   tCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCACCATCCCAGGCTTCTca  >  1:666443/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                                        ATAGCTCAGTCGGTAGAGCAGGGGATTGAAAAT‑CCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCACCATCCCAGGCTTCTCA  >  NC_000913/3110372‑3110641

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑