Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,030,748	A→G	11.1%	intergenic (+34/‑461)	PP_4433 → / → dadA‑I	amino acid MFS transporter/D‑amino acid dehydrogenase small subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,030,748	0	A	G	11.1%	112.8 / 5.9	45	intergenic (+34/‑461)	PP_4433/dadA‑I	amino acid MFS transporter/D‑amino acid dehydrogenase small subunit
Reads supporting (aligned to +/- strand):  ref base A (20/20);  new base G (3/2);  total (23/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.41e-01

CACCTGCCTACTACATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTCTTCGCTATCTC  >  NC_002947/5030602‑5030893                                                                                                                                                    |                                                                                                                                                  cACCTGCCTACTACATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAAt                                                                                                                                                 <  5:317864/149‑1 (MQ=255)  aCCTGCCTACTACATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAAt                                                                                                                                                 >  1:324991/1‑148 (MQ=255)  aCCTGCCTACTACATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATc                                                                                                                                                <  5:73751/149‑1 (MQ=255)      gCCTACTACATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCa                                                                                                                                            >  6:215803/1‑149 (MQ=255)       ccTACTACATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCAc                                                                                                                                           >  2:69545/1‑149 (MQ=255)          actacATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCAcc                                                                                                                                          >  3:348915/1‑147 (MQ=255)                  atGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGtt                                                                                                                                 <  5:215803/148‑1 (MQ=255)                  atGGGTGCATCAGCACTTGGCATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGTGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGTTAATCAGCACCCAGGCTGtt                                                                                                                                 <  6:355651/148‑1 (MQ=255)                              gCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGCAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCAt                                                                                                                     <  1:69545/149‑1 (MQ=255)                                    gggATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATtcctcc                                                                                                               <  5:237112/148‑1 (MQ=255)                                      gATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCggg                                                                                                            >  6:229113/1‑149 (MQ=255)                                             gCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGcc                                                                                                      <  5:297882/148‑1 (MQ=255)                                                ttgttCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGGAGATGGTATAG‑AGCCTGGTTGCTATTCATCACACAGGCTTTTGCGAAGCTCCATTCCTCCGGGCAAGCCGa                                                                                                    >  7:221284/1‑147 (MQ=255)                                                        tgtgATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGt                                                                                          >  4:246187/1‑149 (MQ=255)                                                         gtgATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTc                                                                                         >  1:13797/1‑149 (MQ=255)                                                                agaCTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATaa                                                                                  <  5:229113/149‑1 (MQ=255)                                                                      aaGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAagcag                                                                              <  2:324991/147‑1 (MQ=255)                                                                      aaGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAagc                                                                                >  3:248135/1‑145 (MQ=255)                                                                      aaGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAagc                                                                                <  4:248135/145‑1 (MQ=255)                                                                              tCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCa                                                                    >  2:64875/1‑149 (MQ=255)                                                                              tCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCa                                                                    >  6:216194/1‑149 (MQ=255)                                                                                gATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCAcc                                                                  >  4:219723/1‑149 (MQ=255)                                                                                           aTGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTa                                                       <  3:246187/149‑1 (MQ=255)                                                                                                   ccTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCttt                                                          <  4:264003/138‑1 (MQ=255)                                                                                                   ccTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCttt                                                          >  3:264003/1‑138 (MQ=255)                                                                                                          cAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCCCCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACctc                                        >  5:304312/1‑149 (MQ=255)                                                                                                            aaaTAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCtt                                      <  6:50860/149‑1 (MQ=255)                                                                                                             aaTAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCTCCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTg                                     <  2:13797/149‑1 (MQ=255)                                                                                                             aaTAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTg                                     >  5:38330/1‑149 (MQ=255)                                                                                                               tAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTgg                                    >  5:218028/1‑148 (MQ=255)                                                                                                                aaCCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTTCGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCa                                  >  8:135732/1‑149 (MQ=255)                                                                                                                   cTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCt                               >  3:146410/1‑149 (MQ=255)                                                                                                                           cAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCTGGCCCTGa                       <  5:216194/149‑1 (MQ=255)                                                                                                                                 gTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCTGGCCCTGATAACa                  <  6:218028/148‑1 (MQ=255)                                                                                                                                    taG‑AGCCTGTGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGTCAAGCCGACCGGCTACTTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCTGGCCCTGATAACAgtg               <  8:221284/148‑1 (MQ=255)                                                                                                                                         gCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTCTTc          <  3:219723/149‑1 (MQ=255)                                                                                                                                           cTGGGTGCTGATTAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCTGGccc                          <  4:248529/131‑1 (MQ=255)                                                                                                                                           cTGGGTGCTGATTAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCTGGccc                          >  3:248529/1‑131 (MQ=255)                                                                                                                                           cTGGGTGCTGATTAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTCTTCGc        >  7:216802/1‑149 (MQ=255)                                                                                                                                             gggTGCTGATTAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTc                                                                      <  1:25856/85‑1 (MQ=255)                                                                                                                                             gggTGCTGATTAGCACCCAGGCTGTTGCGAAGCTCAATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTc                                                                      >  2:25856/1‑85 (MQ=39)                                                                                                                                              ggTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTCTTCGCTAt     >  2:310015/1‑149 (MQ=255)                                                                                                                                                 gCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTa                                                 <  7:168457/102‑1 (MQ=255)                                                                                                                                                 gCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTa                                                 >  8:168457/1‑102 (MQ=255)                                                                                                                                                  cTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTCTTCGCTAtctc  <  6:38330/148‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                  CACCTGCCTACTACATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAG‑AGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTCTTCGCTATCTC  >  NC_002947/5030602‑5030893

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑