Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	337,816:1	+A	12.5%	intergenic (‑66/+63)	PP_0279 ← / ← PP_0280	hypothetical protein/amino acid ABC transporter permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	337,816	1	.	A	12.5%	165.8 / 20.4	48	intergenic (‑66/+63)	PP_0279/PP_0280	hypothetical protein/amino acid ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base . (22/20);  new base A (4/2);  total (26/22)
Fisher's exact test for biased strand distribution p-value = 6.74e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.11e-01

GTGCTCGATCAGGAACTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAACGAGATCACCAGGT  >  NC_002947/337679‑337961                                                                                                                                             |                                                                                                                                                  gTGCTCGATCAGGAACTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGt                                                                                                                                        <  7:350425/149‑1 (MQ=255) gTGCTCGATCAGGAACTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGt                                                                                                                                        >  7:86761/1‑149 (MQ=255)       gATCAGGAACTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGgcgc                                                                                                                                  >  1:9068/1‑149 (MQ=255)        aTCAGGAACTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGGC‑ACATTCAAGGTTGgcgc                                                                                                                                  >  2:120201/1‑148 (MQ=255)         tCAGGAACTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTa                                                                                                                                >  8:268655/1‑149 (MQ=255)              aaCTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTGTAGCGCCAACCTTGAATG‑TGGCGCTATACCt                                                                                                                           <  3:32294/149‑1 (MQ=25)              aaCTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCt                                                                                                                           <  2:9068/149‑1 (MQ=255)               aCTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCACACAGGTATAGCGCC‑ACATTAAACGTTGGCGCTACAccgc                                                                                                                          >  7:186163/1‑147 (MQ=255)                            cTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGt                                                                                                             <  7:207371/149‑1 (MQ=255)                                aaGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGccc                                                                                                         >  7:119635/1‑149 (MQ=255)                                         cTTAGGTGGGGGCTGTGGAGGTGGTTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGcag                                                                                                >  5:274684/1‑149 (MQ=255)                                          ttcggTGGGGGCTTGGGAGGGGGTTGGGCT‑TGGCAAGTATGTGTGGGGGTTTTGCGGGCCTC‑TTCGCGGGCACGCCCGCTCCAACCTGTATCGCGCC‑ACATTCATGGTTGGCGCTACCCCTGTGGGAGCGGGCGTGCCCGCGAAGcagt                                                                                               <  6:174620/146‑1 (MQ=25)                                          ttAGGTGGGGGCTGTGGAGGTGGTTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACCGGTATAGCGCC‑ACAATCAAAGTTGGCGCTACACCAGTGGGACCCGGCGTGCCCGCGAAGcaa                                                                                                >  5:2141/1‑147 (MQ=38)                                          ttAGGGGGGGGCTGGGGAGGGGGTGGGGCA‑TGGCACGGATGGGTGGTGGTTTTGAGGGCCTC‑TGCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGcagt                                                                                               <  5:366113/149‑1 (MQ=37)                                                gggggCTGTGGAGGTGGTTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAACGCC‑ACATTCAAGGTTGGAGCTAAACAAGTGGGAGAGGGCGTGCCCGCGAAGcagtcagt                                                                                           >  7:53964/1‑147 (MQ=38)                                                 ggggCTGTGGAGGTGGTTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTAAAGCGCC‑ACATTCACGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAg                                                                                        <  1:120201/149‑1 (MQ=255)                                                   ggCTGGGGAGGGGGTTGGGCA‑TGCCACGGAGGGGGGGGGGTTTGGAGGCCCTC‑TTCGCGGGCCCGCCCGCTCCCACTGGTATAGCGCA‑ACATTCACGGTGGGCGCTACCCCTGTGGGAGCGGGCGTGCCCGCGaa                                                                                                    <  6:226872/135‑1 (MQ=21)                                                          gAGGTGGTTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCtgt                                                                                                                         <  4:106532/107‑1 (MQ=255)                                                          gAGGTGGTTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCtgt                                                                                                                         >  3:106532/1‑107 (MQ=255)                                                              gggtTTGGCATTGGCTTGGTTGGGTGGTGGTTTTG‑CGGCCTCGTTGGCGGGAAGGCCCGCGCCCACCTTTATAGCCCT‑ATTTTCAGGGTTGGGGTTACAGGTGTGGTTGGGGGGGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGcc                                                                            <  6:2141/148‑1 (MQ=255)                                                               ggtTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCtt                                                                          >  6:188604/1‑149 (MQ=255)                                                                gtTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGc                                                                                                           >  7:313489/1‑115 (MQ=255)                                                                     cctatctcAAGGTTGTGTGGTGGTTTTGCGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTGGGCGCTACACGTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTggca                                                                      <  5:360683/141‑1 (MQ=37)                                                                                gagggttggtggTTTTGAGGGCCGC‑TTCGCGGGCACGCCCGCTCGCACAGGTATAGCGCC‑ACATTCAAGGTTGGGGCTACACCTGTGGGTGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCAcgc                                                           <  8:186163/142‑1 (MQ=38)                                                                                 aTGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGc                                                                                                               >  7:293439/1‑95 (MQ=255)                                                                                 aTGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGc                                                                                                               <  8:293439/95‑1 (MQ=255)                                                                                     gtggtgGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCACCCACAGGTATAGCGCC‑ACAATCAAAGTTTGGGGTAACCCAGTGGGAGCGGGCGAGCCCGCGAAGCAGTCAGTGCGGTCTCACCGGCCGTGGGAGGCAGACCCgcgcca                                                       >  8:328010/1‑145 (MQ=21)                                                                                     gtggtgGTTTTCCGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCCCC‑ACATTCATGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACgcgc                                                         <  7:328010/145‑1 (MQ=255)                                                                                      tggtggTTTTGAGGGCCTC‑TTCGCGGGAACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAAc                                                      >  6:369247/1‑147 (MQ=255)                                                                                        gtggtTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTggcaggc                                                                   >  3:162707/1‑132 (MQ=255)                                                                                            ttttGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTc                                              <  8:119635/149‑1 (MQ=255)                                                                                               tGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCca                                            <  7:268655/148‑1 (MQ=255)                                                                                                 aGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCcagca                                         >  6:186248/1‑149 (MQ=255)                                                                                                     ccTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCCGCGGCCTTGGCAGGCCTCCCCGCGCAACCAGCGCTCCAGCAGCtt                                     >  7:77239/1‑149 (MQ=255)                                                                                                      tgc‑tTCGCGGGCACGCCCGCTCCCACAGGTGTAGCGCCAACCTTGAATG‑TGGCGCTATACCTGTGGGAGCGGGCGTGCCCGCGAAGCCGTCAGGGAGGTCTCCGCGGCCTTGGCAGGCCTCCACGCGCCACCAGCGCTCCAGCCGCGTg                                    >  5:131280/3‑149 (MQ=14)                                                                                                            cgcgGGAACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGaa                                  <  5:369247/146‑1 (MQ=255)                                                                                                             gcgGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAAcc                               <  6:274684/148‑1 (MQ=255)                                                                                                              cggccccGCCCGCTCCCACTGGTATAGCGCC‑ACATTCACGGTTGGCGATACACGTGTGGGAGGGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCtt                             <  3:58886/143‑1 (MQ=255)                                                                                                               gggCACGCCCGCTCCCACAGGTGTAGCGCCAACCGTGAATG‑TGGCGCTATACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTGAGTGAGGGCTCAGCGGCCTTGGCAGGCCTCCACGCGCCACCAGCGCTCCCGCAGCTTGAAGCCTTg                            >  2:196316/1‑149 (MQ=17)                                                                                                                       ccGCTCCCACAGGAATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCa                    >  5:350470/1‑149 (MQ=255)                                                                                                                        cGCTCCCACAGGTGTAGCGCCAACCTTGAATG‑TGGCGCTATACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCtt                             >  4:245843/1‑139 (MQ=21)                                                                                                                             ccACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAAc               >  1:41281/1‑148 (MQ=255)                                                                                                                             ccACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAAc               >  7:254508/1‑148 (MQ=255)                                                                                                                             ccACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAAc               >  6:244747/1‑148 (MQ=255)                                                                                                                               acaGGTGTAGCGCCAACCTTGAATG‑TGGCGCTATACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTg                            >  4:140418/1‑133 (MQ=21)                                                                                                                               acaGGTGTAGCGCCAACCTTGAATG‑TGGCGCTATACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTg                            <  3:140418/133‑1 (MQ=21)                                                                                                                                caGGTATAGCGCC‑ACATTCAAGGTGGGCGCTACACCTGGGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAACgaga           <  2:257139/149‑1 (MQ=255)                                                                                                                                         cgcC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAACGAGATCACCAGGt  <  5:188604/149‑1 (MQ=255)                                                                                                                                           cc‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAACGAGATCACCAgg   >  2:294765/1‑146 (MQ=255)                                                                                                                                             |                                                                                                                                                  GTGCTCGATCAGGAACTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCA‑TGGCAAGGATGTGTGGTGGTTTTGAGGGCCTC‑TTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAACGAGATCACCAGGT  >  NC_002947/337679‑337961

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑