Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,560,455	+G	intergenic (‑2/+1)	glpR ← / ← glpR	pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,560,455	1	.	G	97.6%	156.9 / ‑3.6	41	intergenic (‑2/+1)	glpR/glpR	pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base G (18/22);  total (19/22)
Fisher's exact test for biased strand distribution p-value = 4.63e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTG  >  NC_000913/3560305‑3560595                                                                                                                                                         |                                                                                                                                             gtgCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGc                                                                                                                                               >  1:1041676/1‑151 (MQ=255)       atatCGATAAACGGCGTCGAGCCTTTGGGGATTGGCCCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGcgcag                                                                                                                                           <  1:791072/149‑5 (MQ=255)             aTAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGt                                                                                                                                   >  2:450150/1‑151 (MQ=255)                   aGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCt                                                                                                                             >  2:2462221/1‑151 (MQ=255)                      gTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTca                                                                                                                           <  1:1118467/150‑2 (MQ=255)                              aTTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTc                                                                                                                   >  2:1172268/1‑150 (MQ=255)                                 ggggTTTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTg                                                                                                               <  1:450166/151‑1 (MQ=255)                                   ggATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTg                                                                                                               >  1:2873193/1‑149 (MQ=255)                                      tttGCTCCGCCTCTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAgg                                                                                                            <  1:549819/149‑1 (MQ=255)                                       ttGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTc                                                                                                          <  1:1403417/150‑1 (MQ=255)                                         gCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTcgcg                                                                                                       >  1:58965/1‑151 (MQ=255)                                            ccGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcggc                                                                                                     <  2:1041984/150‑1 (MQ=255)                                                cACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATa                                                                                                <  2:3391305/151‑1 (MQ=255)                                                cACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGAGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAAt                                                                                                 >  2:3766923/1‑150 (MQ=255)                                                 aCTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGcc                                                                                                                        >  2:119217/1‑126 (MQ=255)                                                  cTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGcc                                                                                                                        <  1:119222/125‑1 (MQ=255)                                                   tttGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTc                                                                                             >  2:205294/1‑151 (MQ=255)                                                     tGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTg                                                                                           >  1:1710843/1‑151 (MQ=255)                                                      gCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGc                                                                                          <  2:2955964/151‑1 (MQ=255)                                                         ggCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCggg                                                                                       >  2:2041027/1‑151 (MQ=255)                                                            gATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTg                                                                                    >  2:2271909/1‑151 (MQ=255)                                                               gcgcTCTTTTTCTTCGGTCGGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACGGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACg                                                                                 <  1:1504799/151‑1 (MQ=255)                                                                    ctTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGgaga                                                                             >  2:3595056/1‑150 (MQ=255)                                                                       tttCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAAt                                                                          <  2:213114/150‑1 (MQ=255)                                                                          gttcGGGCTGGGGGGCCTTGCGGGAATGGCGGGGCGTGTTAAGGGAAATGGATGGGGGCGCCGCATCGTTATAAAAAAG‑CAGGATAAGGATTTGATCAGCCAGATCAATGAGGTCGCGGCGAATAGTATGCGGGCTGACGGAGAAATg                                                                         >  1:286619/2‑148 (MQ=255)                                                                                 cTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGc                                                               >  2:3709806/1‑151 (MQ=255)                                                                                   gggTGCCCTTGGGATCGGGCCACGGCGTTTTAGCCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAg                                                                <  2:1245916/148‑1 (MQ=255)                                                                                     gTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCtt                                                           <  2:779593/151‑1 (MQ=255)                                                                                       ggCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCg                                                         <  1:2128039/151‑1 (MQ=255)                                                                                            tGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACt                                                    >  2:3265596/1‑151 (MQ=255)                                                                                             gCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTg                                                   >  1:257490/1‑151 (MQ=255)                                                                                               gATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCCGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGAc                                                 >  2:589688/1‑151 (MQ=255)                                                                                                      ccACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAccc                                          >  2:1017508/1‑151 (MQ=255)                                                                                                             gtgtTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGtt                                   <  1:2554022/151‑1 (MQ=255)                                                                                                                ttAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGATTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGttt                                  >  1:3452385/1‑149 (MQ=255)                                                                                                                       aaCTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGtt                          <  1:1504486/150‑1 (MQ=255)                                                                                                                       aaCTGGAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTc                         <  2:3355816/151‑1 (MQ=255)                                                                                                                           ggAAGGCAGCGCCGCCCCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGat                      <  1:3551226/150‑1 (MQ=255)                                                                                                                           ggAAGGCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGa                       <  2:886020/149‑1 (MQ=255)                                                                                                                               ggCAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGataata                  <  1:3158794/150‑1 (MQ=255)                                                                                                                                 cAGCGCCGCACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATAcc                <  1:3265390/150‑1 (MQ=255)                                                                                                                                       cgcACCGCCAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGa         <  1:3521092/151‑1 (MQ=255)                                                                                                                                              ccAT‑GATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTtgtg  <  1:1144117/151‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                             GTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAT‑GATGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTG  >  NC_000913/3560305‑3560595

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑