Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,506,934	C→T	15.9%	intergenic (+55/‑62)	petC → / → sspA	ubiquinol‑‑cytochrome c reductase cytochrome c1 subunit/stringent starvation protein A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,506,934	0	C	T	15.9%	82.8 / 7.8	38	intergenic (+55/‑62)	petC/sspA	ubiquinol‑‑cytochrome c reductase cytochrome c1 subunit/stringent starvation protein A
Reads supporting (aligned to +/- strand):  ref base C (18/13);  new base T (4/2);  total (22/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.29e-01

CGCATCGGCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGCCGAGAAGGGC  >  NC_002947/1506790‑1507082                                                                                                                                                 |                                                                                                                                                      cgcATCGTCACGTATGTGTTGCTGTATTTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCTAGAGTGAATGCTGGAAGGACTTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGTGGTGGACTAGCAGTATTGCAAGGc                                                                                                                                                   <  3:188570/149‑1 (MQ=255) cgcATCGGCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGc                                                                                                                                                   <  6:109806/149‑1 (MQ=255) cgcATCGGCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGc                                                                                                                                                   <  7:25938/149‑1 (MQ=255)        gCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCg                                                                                                                                            >  8:113443/1‑149 (MQ=255)             tATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGg‑cgc                                                                                                                                      >  7:183825/1‑149 (MQ=255)               tgtgTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCATGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGt                                                                                                                                    <  7:113443/149‑1 (MQ=255)                   ttGCTGTAGCTGGCTTTCTTCTTCGTATTCGCCTACTTGCGCAAGCGGGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTc                                                                                                                                <  7:181840/149‑1 (MQ=255)                                               tCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGc                                                                                                      >  2:30922/1‑147 (MQ=255)                                                  ccTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCTTTTAAAGTTGCACAAGCATCCGTGCgagga                                                                                                 <  1:30922/149‑1 (MQ=255)                                                  ccTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCgagga                                                                                                 <  8:183825/149‑1 (MQ=255)                                                   cTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCgaggag                                                                                                >  4:139692/1‑149 (MQ=255)                                                             aaGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTGGCAATACTGCTAGGc                                                                                                                                                   <  1:1257/89‑1 (MQ=37)                                                             aaGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTGGCAATACTGCTAGGc                                                                                                                                                   >  2:1257/1‑89 (MQ=37)                                                                          ggAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGcaaccaa                                                                           >  7:181702/1‑147 (MQ=255)                                                                                          aTCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGgc                                                                                   >  3:335282/1‑123 (MQ=255)                                                                                          aTCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGgc                                                                                   <  4:335282/123‑1 (MQ=255)                                                                                                           ggTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACt                                        >  3:184814/1‑149 (MQ=255)                                                                                                               gttgAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTAtt                                     <  8:181702/148‑1 (MQ=255)                                                                                                                     cgcgCCAGGGGTGGCCTAGAAGAATTGCCAGGCCACCCCGGG‑CGCCTTTTCATTTAAAGTTGCACAAGCAAACGTGCGAGGCGCCCCTACATGGGCGCAACCAACAGGATAGCCACCTATTCCCATCCCGATGATCACTAATATCATCg                              >  8:49008/1‑149 (MQ=255)                                                                                                                      gcgcCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGt                                                                                                        >  8:153315/1‑74 (MQ=255)                                                                                                                      gcgcCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGt                                                                                                        <  7:153315/74‑1 (MQ=255)                                                                                                                        gcCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGt                           >  7:112979/1‑149 (MQ=255)                                                                                                                         cccGGGGTGGCCTAGCAGTATTGCCAGGTCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGtt                          >  3:322929/1‑149 (MQ=255)                                                                                                                              ggTGGCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCt                     <  4:184814/149‑1 (MQ=255)                                                                                                                                  gCCTGGCAATACTGCTAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTAtt                                     >  4:14242/1‑129 (MQ=255)                                                                                                                                  gCCTGGCAATACTGCTAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTAtt                                     <  3:14242/129‑1 (MQ=255)                                                                                                                                  gCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGtt                 >  5:194694/1‑149 (MQ=255)                                                                                                                                  gCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGt                  <  1:345233/148‑1 (MQ=255)                                                                                                                                  gCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGt                  >  8:276062/1‑148 (MQ=255)                                                                                                                                      ggCAATACTGCTAGGCCACCCCGGGCCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGGGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTGTTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTg              >  1:185758/2‑149 (MQ=255)                                                                                                                                       gCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGc            <  8:112979/149‑1 (MQ=255)                                                                                                                                       gCAATACTGCTAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGc            >  7:275107/1‑149 (MQ=255)                                                                                                                                         aGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGcc           >  2:33663/1‑148 (MQ=255)                                                                                                                                          gTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGCGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGcc           >  5:253333/1‑147 (MQ=255)                                                                                                                                             ttGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGCCgag        >  1:333697/1‑147 (MQ=255)                                                                                                                                             ttGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCGGGTCACGTTTCTCATCGGGTTCGCCGGGTTCTGGCCgag        >  2:134406/1‑147 (MQ=255)                                                                                                                                              tGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGG‑TAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGCCga         >  6:92382/1‑144 (MQ=255)                                                                                                                                              tGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGG‑TAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGCCga         <  5:92382/144‑1 (MQ=255)                                                                                                                                                ccAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGc                                                <  2:249258/104‑1 (MQ=255)                                                                                                                                                ccAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGc                                                >  1:249258/1‑104 (MQ=255)                                                                                                                                                ccAGGCCACCCCGGG‑CGCGGTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACGATTCTCATCGGGTTCGCCTGGTTCTGGCCGAGAAggg   >  6:341159/1‑149 (MQ=255)                                                                                                                                                 cAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGCCGAGAAGGGc  <  6:194694/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                      CGCATCGGCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGG‑CGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGCCGAGAAGGGC  >  NC_002947/1506790‑1507082

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: ‑