Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,110,533	G→A	intergenic (+92/+57)	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	3,110,533	0	G	A	96.5%	88.8 / ‑4.1	29	intergenic (+92/+57)	pheV/yghD	tRNA‑Phe/putative type II secretion system M‑type protein
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (12/16);  total (13/16)
Fisher's exact test for biased strand distribution p-value = 4.48e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.61e-01

TCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCACCATCCCAGGCTTCTCAGCAGCACTGACATCAATTTGTGTCA  >  NC_000913/3110412‑3110666                                                                                                                          |                                                                                                                                      tCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTGCTCTCGCCACGtt                                                                                                                     <  2:719440/140‑1 (MQ=255)    ttGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCTCGTTAAc                                                                                                                  <  2:1117397/140‑1 (MQ=255)    ttGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAAc                                                                                                                  <  1:380653/140‑1 (MQ=255)    ttGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAAc                                                                                                                  <  1:804134/140‑1 (MQ=255)     tGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACg                                                                                                                 >  2:419582/1‑140 (MQ=255)         tCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGagag                                                                                                             <  1:419582/140‑1 (MQ=255)           gATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTa                                                                                                           >  1:776555/1‑140 (MQ=255)                  aGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTAt                                                                                                    <  2:776555/140‑1 (MQ=255)                  aGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTAt                                                                                                    <  1:831620/140‑1 (MQ=255)                       gggCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGata                                                                                               >  1:395294/1‑140 (MQ=255)                           accacTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTaa                                                                                           <  1:168989/140‑1 (MQ=255)                            ccacTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAt                                                                                          <  1:360912/140‑1 (MQ=255)                                 aaTTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCt                                                                                     <  2:59733/140‑1 (MQ=255)                                   ttCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGa                                                                                   <  2:1126916/140‑1 (MQ=255)                                       tAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACt                                                                               >  1:1043059/1‑140 (MQ=255)                                             cccGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTAccc                                                                         >  2:908522/1‑140 (MQ=255)                                                                 ttGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCt                                                     <  1:873542/140‑1 (MQ=255)                                                                  tGCTTTTTGATCTGACAATAACCCTCACGAAAAAAATTAGCTTATAAAATCTTGGGGAATTACTCTCCCCCCGTTAAAGAGAGGAATTTTATTTATATTAATTTCCTGATACTTTACCCCCCTCCAAACTCCAGcccccg                                                    >  2:805741/1‑136 (MQ=255)                                                                      tttGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGcaca                                                <  2:1043059/140‑1 (MQ=255)                                                                       ttGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACAt                                               >  2:1127186/1‑140 (MQ=255)                                                                                          tCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCACCATCCCAGGCTtctc                            >  2:461384/1‑140 (MQ=255)                                                                                          tCACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCACCATCCCAGGCTtctc                            >  1:47566/1‑140 (MQ=255)                                                                                           cACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCACCATCCCAGGCtt                               >  2:269409/1‑136 (MQ=255)                                                                                           cACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCACCATCCCAGGCtt                               <  1:269409/136‑1 (MQ=255)                                                                                           cACGAAAAAAATTAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCACCATCCCAGGCTTCTca                           >  1:793924/1‑140 (MQ=255)                                                                                                       tAGCTTATAAAGTCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCACCATCCCAGGCTTCTCAGCAGCACTGACa               <  1:805741/140‑1 (MQ=255)                                                                                                              aaaaGCCTGGGGAAATTGCTCTCCCCACGTTAACGAAAGTAATTTAATTGATATTAATCTCCTGATACTTTCCCCCCCCCCAACCTCCAGCCGCTGCACATGCGCCTCCCCAGCCTTCTCAGGAGCATGGACACCAAttt        <  2:793924/139‑1 (MQ=255)                                                                                                                   tCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCACCATCCCAGGCTTCTCAGCAGCACTGACa               >  2:6800/1‑128 (MQ=255)                                                                                                                   tCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCACCATCCCAGGCTTCTCAGCAGCACTGACa               <  1:6800/128‑1 (MQ=255)                                                                                                                   tCTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCACCATCCCAGGCTTCTCAGCAGCACTGACATCAATTTGTGTc   >  2:226649/1‑140 (MQ=255)                                                                                                                    cTGGGGAAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCACCATCCCAGGCTTCTCAGCAGCACTGACATCAATTTGTGTCa  >  2:548826/1‑140 (MQ=255)                                                                                                                          |                                                                                                                                      TCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTCCAGCCGCTGCACATTCACCATCCCAGGCTTCTCAGCAGCACTGACATCAATTTGTGTCA  >  NC_000913/3110412‑3110666

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑