Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,143,882	T→A	9.1%	intergenic (+35/‑88)	PP_3647 → / → PP_3648	oxidoreductase/carboxymuconolactone decarboxylase family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,143,882	0	T	A	9.1%	115.1 / 2.6	44	intergenic (+35/‑88)	PP_3647/PP_3648	oxidoreductase/carboxymuconolactone decarboxylase family protein
Reads supporting (aligned to +/- strand):  ref base T (25/15);  new base A (2/2);  total (27/17)
Fisher's exact test for biased strand distribution p-value = 6.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01

GGTGACCACGCGATCATTGTCGGCGCGGTGAAGAACCTGGTGTTGCCTGAGCAGCCGATGACCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCTTTTTTATGCCGGAGTACTGCACATGAGCAATGAAAAGTACGAAAAGGGCCTGAAAATCCGCACCCAGGTACTGGGC  >  NC_002947/4143734‑4144023                                                                                                                                                     |                                                                                                                                               ggTGAACACGCGATCATTGTCGGCGCGGTGAAGCACCTGGTATTGCCTGAGCAGCCGATGACCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCt                                                                                                                                                >  4:264728/1‑149 (MQ=255)     aCCACGCGATCATTGTCGGCGCGGTGAAGAACCTGGTGTTGCCTGAGCAGCCGATGACCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGc                                                                                                                                             <  3:101381/148‑1 (MQ=255)        aCGCGATAATTGTCGGCGCGGTGAAGAAACTGGTGTTGCCTGAGCAGCCGATGACCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCcgc                                                                                                                                         >  4:373237/1‑149 (MQ=255)          gcgATCATTGTCGGCGCGGTGAAGAACCTGGTGTTGCCTGAGCAGCCGATGACCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCAAGCCCGCGa                                                                                                                                       <  4:76528/149‑1 (MQ=255)            gATCATTGTCGGCGCGGTGAAGAACCTGGTGTTGCCTGAGCAGCCGATGACCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCAAGCCcgcg                                                                                                                                        >  3:271569/1‑146 (MQ=255)              tCATTGTCGGCGCGGTGAAGAACCTGGTGTTGCCTGAGCAGCCGATGACCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCAAGCCCGCGAAGAt                                                                                                                                   <  3:5929/149‑1 (MQ=255)                 ttGTCGGCGCGGTGAAGAACCTGGCGTTGCCTGAGCAGCCGATGACCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGcc                                                                                                                                >  6:310131/1‑149 (MQ=255)                    tCGGCGCGGTGAAGAACCTGGCGTTGCCTGAGCAGCCGATGACCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCt                                                                                                                             <  5:310131/149‑1 (MQ=255)                            gTGAATAACCTGGTGTTGCCTGAGCAGCCGATGACCCCGATGTTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAg                                                                                                                     <  1:292359/149‑1 (MQ=255)                            gTGAAGAACCTGGTGTTGCCTGAGCAGCCGATGACCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAg                                                                                                                     <  5:165173/149‑1 (MQ=255)                                ctaaCCTGGTGTTGCCTGAGCAGCCGATGACCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGAAACATCTTGAGTCGAGGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGt                                                                                                                 <  3:188501/147‑1 (MQ=255)                                 gaaCCTGGTGTTGCCTGAGCAGCCGATGACCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTc                                                                                                                >  6:14164/1‑149 (MQ=255)                                   aCCTGGTGTTGCCTGAGCAGCCGATGACCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGt                                                                                                                 >  4:188501/1‑146 (MQ=255)                                    ccTGGTGTTGCCTGAGCAGCCGATGACCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTcgcg                                                                                                             >  7:38177/1‑149 (MQ=255)                                          gtTGCCTGAGCAGCCGATGACCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATc                                                                                                       >  7:328355/1‑149 (MQ=255)                                              ccTGAGCAGCCGATGACCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑Gtct                                                                                                  <  3:373237/149‑1 (MQ=255)                                                     agcCGATGACCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTc                                                                                           >  4:39788/1‑149 (MQ=255)                                                             aCCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCgg                                                                                   <  5:184894/149‑1 (MQ=255)                                                              ccccGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGc                                                                                  >  5:362367/1‑149 (MQ=255)                                                               cccGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGttt                                                                                                                         <  6:344671/110‑1 (MQ=255)                                                               cccGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGttt                                                                                                                         >  5:344671/1‑110 (MQ=255)                                                                  gATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCt                                                                              >  3:186527/1‑149 (MQ=255)                                                                        gtACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCTTTTTTa                                                                        >  3:237603/1‑149 (MQ=255)                                                                            cacaAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTTACCCTCGGTTGCGGCCCCTTTTTTATGcc                                                                    >  5:16027/1‑149 (MQ=255)                                                                             acaAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCTTTTTTATGCCg                                                                   >  4:342381/1‑149 (MQ=255)                                                                              caAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCGTTTTTATGCCg                                                                   >  4:28109/1‑148 (MQ=255)                                                                                           ggCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCTTTTTTATGCCGGAGTACTGCACAt                                                      >  5:106018/1‑148 (MQ=255)                                                                                                  tGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCTTTTTTATGCCGGAGTACTGCACATGAGCAAt                                               >  5:176356/1‑148 (MQ=255)                                                                                                      gccACTTTGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCTTTTTTATGCCGGAGTACTGCACATGAGCAATGaaaa                                          <  5:116387/149‑1 (MQ=255)                                                                                                         aCTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCTTTTTTATGCCGGAGTACTGCACATGAGCAATGAAAAGTa                                       <  3:342381/149‑1 (MQ=255)                                                                                                              gCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCTTTTTTATGCCGGAGTACTGCACATGAGCAATGAAAAGTACGaa                                   >  6:324486/1‑148 (MQ=255)                                                                                                                tGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGtttt                                                                                                                        <  1:137/62‑1 (MQ=255)                                                                                                                tGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGtttt                                                                                                                        >  2:137/1‑62 (MQ=255)                                                                                                                       tCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCACGAGAAGATGCACATGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCATTTTTATTCAGGAGTACTGAACATGAGCAATGAAAAGTACGAAAAGGGCCTg                          >  2:264065/1‑148 (MQ=255)                                                                                                                         ttGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCTTTTTTATGCCGGAGTACTGCACAt                                                      <  7:190738/118‑1 (MQ=255)                                                                                                                         ttGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCTTTTTTATGCCGGAGTACTGCACAt                                                      >  8:190738/1‑118 (MQ=255)                                                                                                                             gTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCTTTTTTATGCCGGAGTACTGCACATGAGCAATGAAAAGTACGAAAAGGGCCTGAAAATcc                   >  2:342029/1‑149 (MQ=255)                                                                                                                              tCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCTTTTTTATGCCGGAGTACTGCACATGAGCAATGAAAAGTACGAAAAGGGCCTGAAAATcc                   <  4:186527/148‑1 (MQ=255)                                                                                                                              tCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCTTTTTTATGCCGGAGTACTGCACATGAGCAATGAAAAGTACGAAAAGGGCCTGAAAATCCg                  >  4:89669/1‑149 (MQ=255)                                                                                                                                       gCATCTTCGCGGGCAAGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCTTTTTTATGCCGGAGTACTGCACATGAGCAATGAAAAGTACGAAAAGGGCCTGAAAATCCGCACCCAgg          >  3:121443/1‑148 (MQ=255)                                                                                                                                            ttCGCGGGCTTGCCCGCGAAGATGCCGGTGTTTTCAGGGGTCGCGCTAATC‑GTCTCCCCCTCGGTTGCGGCCCCTTTTTTATGCCGGAGTACTGCACAGGAGCAATGAAAAGTACGAAAAGGGCCTGAAAATCCGCACCCAGGtcgtgg    >  5:203960/1‑144 (MQ=255)                                                                                                                                            ttCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCTTTTTTATGCCGGAGTACTGCACATGAGCAATGAAAAGTACGAAAAGGGCCTGAGAATCCGCCCCCAGGTagggg    >  8:278228/1‑145 (MQ=255)                                                                                                                                             tCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATCGGGCTCACCCTCGGTTGCGGCCCCTTTTTTATGCCGGAGTACTGCACATGAGCAATGAAAAGTACGAAAAGGGCCTGAAAATCCGCACCCAGGTACTgg    >  1:291124/1‑149 (MQ=255)                                                                                                                                               gcgGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCTTTTTTATGCCGGAGTACTGCACATGAGCAATGAAAAGTACGAAAAGGGCCTGAAAATCCGCACCCAGGTACTGGGc  <  8:38177/148‑1 (MQ=255)                                                                                                                                               gcgGGCTTGCCAGCGAAGATGCCACTTTTTTCAGGGGTCGCTCTAATC‑GTCTCACCCTCGGTTGCGTGCCCTTTTTTATGCCGGAGTACTGCACATGAGCAATGAAAAGTACGAAAAGGTCCTGAAAATCCGCACCCAGGTACTGGGc  <  3:264728/148‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                               GGTGACCACGCGATCATTGTCGGCGCGGTGAAGAACCTGGTGTTGCCTGAGCAGCCGATGACCCCGATGGTGTACCACAAGGGCAAGCTCGGCGCCCTGCCGCCACTTGGCTGATACATCTTGAGTCGATGTTGGCATCTTCGCGGGCTTGCCCGCGAAGATGCCCCTGTTTTCAGGGGTCGCGCTAATC‑GTCTCACCCTCGGTTGCGGCCCCTTTTTTATGCCGGAGTACTGCACATGAGCAATGAAAAGTACGAAAAGGGCCTGAAAATCCGCACCCAGGTACTGGGC  >  NC_002947/4143734‑4144023

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: ‑