Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,506,934	C→T	12.5%	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	12.5%	101.0 / 5.5	40	intergenic (+55/‑62)	petC/sspA	ubiquinol‑‑cytochrome c reductase cytochrome c1 subunit/stringent starvation protein A
Reads supporting (aligned to +/- strand):  ref base C (20/15);  new base T (2/3);  total (22/18)
Fisher's exact test for biased strand distribution p-value = 6.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.92e-01

AGCGCATCGGCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGCCGAGAAGGGC  >  NC_002947/1506788‑1507082                                                                                                                                                   |                                                                                                                                                     aGCGCATCGGCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTGGCAATACTGCTAg                                                                                                                                                    <  5:329168/149‑1 (MQ=255) aGCGCATCGGCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAg                                                                                                                                                    <  8:120079/149‑1 (MQ=255)   cgcATCGGCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGc                                                                                                                                                  <  7:186583/149‑1 (MQ=255)   cgcATCGGCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGc                                                                                                                                                  <  4:102909/149‑1 (MQ=255)       tCGGCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTGGCAATACTGCTAGGCCAcc                                                                                                                                              <  4:277773/149‑1 (MQ=255)             ccTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTGGCAATACTGCTAGGCCACCCCGGgc                                                                                                                                        <  6:172673/149‑1 (MQ=255)                         tGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGgc                                                                                                                                        <  1:158456/137‑1 (MQ=255)                         tGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGgc                                                                                                                                        >  2:158456/1‑137 (MQ=255)                             tCTGGCTTTCTTCTTCGTATACGCCTACTTGCTCAAGCGCTAATCCTGCAAGGACGTGCACTGATCACGCAGTCGTTTCTGGTTGTTCACCGCGCCCGGGGGGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTaaa                                                                                                                         <  8:327147/148‑1 (MQ=255)                                   tttCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGc                                                                                                                                                  <  4:145654/117‑1 (MQ=255)                                   tttCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGc                                                                                                                                                  >  3:145654/1‑117 (MQ=255)                                       ttcttcTTATTCGCCTACTTGCACAAGCCTGAATACTGGAAGGACGTCCACTGATCACTCAGTAGTTTCTGGTTGTTGAACGCGCCCGGCGTGGCCTAGCACTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAAATGAACaaa                                                                                                               >  2:307643/1‑147 (MQ=255)                                       ttcttcGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTc                                                                                                                                <  7:310223/131‑1 (MQ=255)                                       ttcttcGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTc                                                                                                                                >  8:310223/1‑131 (MQ=255)                                         cttcGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGc                                                                                                              <  1:251751/147‑1 (MQ=255)                                              tATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTg                                                                                                       >  3:242185/1‑149 (MQ=255)                                                                 gCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATggg                                                                                    >  6:212350/1‑149 (MQ=255)                                                                  cgttattACTGGAAGGACGTGCACTGATCACTGAGTTGTTTCTGGTTGTTGCTCGCTCCAGGGGTGGCCTAGCAGTATTCCCAGGCCACCCCGGGCGCGTTTTCATTAAAAGTTGCACATGCATCCGTGCGAGGAGCCGCTACATGGgc                                                                                   <  1:307643/143‑1 (MQ=255)                                                                                          tGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGGTTTGATTTAAAGTTGGACCAGCATGCCTGCGAGGAGCCGGTACATGGGCGCCACCAACAGGTTAGCCTGCTAt                                                           >  6:31148/1‑149 (MQ=255)                                                                                                cGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTCCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGAt                                                     <  6:231496/149‑1 (MQ=255)                                                                                                 gCAGTAGGTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATc                                                    <  5:31148/149‑1 (MQ=255)                                                                                                            tGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCAc                                         >  3:13029/1‑149 (MQ=255)                                                                                                             ggTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATACCGCTGATCAc                                         >  4:119062/1‑148 (MQ=255)                                                                                                                  ttgAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGGTTTCATTTAAAGTTGCGCAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATtct                                   >  7:355146/1‑149 (MQ=255)                                                                                                                       cgcgCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCg                              >  5:305174/1‑149 (MQ=255)                                                                                                                          gcCCGGGGTGGCCTGGCAATACTGCTAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGt                           >  1:52037/1‑149 (MQ=255)                                                                                                                          gcCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTc                                                         >  3:324437/1‑119 (MQ=255)                                                                                                                          gcCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTc                                                         <  4:324437/119‑1 (MQ=255)                                                                                                                           cccGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGtt                          <  5:212350/149‑1 (MQ=255)                                                                                                                                    gCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGtt                 >  7:23815/1‑149 (MQ=255)                                                                                                                                      cTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTTAAGTTGCACAAGCATACGTGCGAGGAGCCGCGACATGGGCGCAACCAAAAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCt               >  1:163701/1‑149 (MQ=255)                                                                                                                                      cTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGATGAGCCGCTACATGGGCCCAACCAACAGGTTAGCCTGCTATTACGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCt               >  3:190594/1‑149 (MQ=255)                                                                                                                                      cTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGcaaccaa                                                                           <  2:14874/89‑1 (MQ=255)                                                                                                                                      cTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGcaaccaa                                                                           >  1:14874/1‑89 (MQ=255)                                                                                                                                       tAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCt                                                                <  2:331981/99‑1 (MQ=255)                                                                                                                                       tAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCt                                                                >  1:331981/1‑99 (MQ=255)                                                                                                                                       tAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTg              >  2:160126/1‑149 (MQ=255)                                                                                                                                         gCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGc            >  5:240519/1‑149 (MQ=255)                                                                                                                                         gCAATACTGCTAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTGCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGc            >  1:343496/1‑149 (MQ=255)                                                                                                                                          cAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGcc           >  8:254379/1‑149 (MQ=255)                                                                                                                                                  ccAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGCCGAGAAgg    <  4:13029/148‑1 (MQ=255)                                                                                                                                                   cAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGtt                 >  7:43510/1‑134 (MQ=255)                                                                                                                                                   cAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGtt                 <  8:43510/134‑1 (MQ=255)                                                                                                                                                   cAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGCCGAGAAGGGc  >  3:375535/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                     AGCGCATCGGCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGCCGAGAAGGGC  >  NC_002947/1506788‑1507082

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: ‑