Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,067,220	T→A	intergenic (‑47/+120)	ygfI ← / ← yggE	putative DNA‑binding transcriptional regulator YgfI/DUF541 domain‑containing protein YggE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,067,220	0	T	A	96.8%	95.8 / ‑5.7	31	intergenic (‑47/+120)	ygfI/yggE	putative DNA‑binding transcriptional regulator YgfI/DUF541 domain‑containing protein YggE
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base A (19/11);  minor base C (1/0);  total (20/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.00e-01

GAGGCTGATATTATTATCTTTGCGGGTAAATAGCGTATAGCCAATTTGTTCTTCCAGCGCGGCAATGCTTTTACCAAATGGCGAAGCCGTCATATGGATTTTTTCTGCCGCCCGGGCAATATTATTGGTTTGCGCTAATAAAATGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTATCCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATCGGGTAAAGGCATTAGCCCGACGAATACGTCGGGCTACAAATATTATTGTGCTGCAGGTGTTTTAGCGGGTTGTTGATCCACAGGTTCTAACTGGAAGACCACATCGACCTGATCATCAAACTGAATAGCGGCCTGCTCGTAAGTTTCCTGGGCGGACACCGGCGCGGC  >  NC_000913/3066994‑3067465                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                      gAGGCTGATATTATTATCTTTGCGGGTAAATAGCGTATAGCCAATTTGTTCTTCCAGCGCGGCAATGCTTTTACCAAATGGCGAAGCCGTCATATGGATTTTTTCTGCCGCCCGGGCAATATTATTGGTTTGCGCTAATAAAATGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCaa                                                                                                                                                                                                                                  >  1:23931/1‑248 (MQ=255)             attatCTTTGCGGGTAAATAGCGTATAGCCAATTTGTTCTTCCATCGCGGCAATGCTTTTTCCAAATGGCGAAGCCGTCATATGGATTTTTTCTGCCGCCCGGGCAATATTATTGGTTTGCGCGAATAAAATGAAATTGCGCATCTTTGTCGAAATAAAAATGTCCATCCCCCTCCCCCGCCTCCTTGTCCGCTTAACCGTTGCAGTCAGCCTAACCTTGAGGAAACCGCGAGCAAAGATAGGTGATTAc                                                                                                                                                                                                                    <  2:343439/250‑1 (MQ=255)                     tGCGGGTAAATAGCGTATAGCCAATTTGTTCTTCCAGCGCGGCAATGCTTTTACCAAATGGCGAAGCCGTCATATGGATTTTTTCTGCCGCCCGGGCAATATTATTGGTTTGCGCTAATAAAATGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGt                                                                                                                                                                                                            <  1:169020/250‑1 (MQ=255)                       cGGGTAAATAGCGTATAGCCAATTTGTTCTTCCAGCGCGGCAATGCTTTTACCAAATGGCGAAGCCGTCATATGGATTTTTTCTGCCGCCCGGGCAATATTATTGGTTTGCGCTAATAAAATGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGCGCAAAGATAGGAGATTACGTCATGGtttt                                                                                                                                                                                                         >  2:349641/1‑251 (MQ=255)                                     ataGCCAATTTGTTCTTCCAGCGCGGCAATGCTTTTACCAAATGGCGAAGCCGTCATATGGATTTTTTCTGCCGCCCGGGCAATATTATTGGTTTGCGCTAATAAAATGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTttacagaaaattaca                                                                                                                                                                                            <  1:145373/250‑1 (MQ=255)                                         ccAATTTGTTCTTCCAGCGCGGCAATGCTTTGACCAAATGGCGAAGCCTTCATATGGATCTATTCTGCCGCCCGGGCAATATTATTGGTTTGCGCTAATAAAATGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAATATAGGCGATTACGTCATGGTTttacagacaattacagaaaa                                                                                                                                                                                       <  2:166509/251‑1 (MQ=255)                                                gTTCTTCCAGCGCGGCAATGCTTTTACCAAATGGCGAAGCCGTCATATGGATTTTTTCTGCCGCCCGGGCAATATTATTGGTTTGCGCTAATAAAATGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGACACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGc                                                                                                                                                                                >  1:82482/1‑251 (MQ=255)                                                     tcCAGCGCGGCAATGCTTTTACCAAATGGCGAAGCCGTCATATGGATTTTTTCTGCCGCCCGGGCAATATTATTGGTTTGCGCTAATAAAATGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACTTCATGGTTTTTCAGAAAAGTACAGAAAAAGGAGGCAata                                                                                                                                                                            <  2:19884/250‑1 (MQ=255)                                                                       ttACCAAATGGCGACGCCGTCATATGGATTTTTTCTGCCGCCCGGGCAATATTATTGGTTTGCGCTAATAAAATGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATCGGGTAAAGGCATTAGcc                                                                                                                                                         >  1:314545/1‑251 (MQ=255)                                                                           cAAATGGCGAAGCCGTCATATGGATTTTTTCTGCCGCCCGGGCAATATTATTGGTTTGCGCTAATAAAATGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATCGGGTAAAGGCATTAGCCcgac                                                                                                                                                     <  1:327039/251‑1 (MQ=255)                                                                                      gCCGTCATATGGATTTTTTCTGCCGCCCGGGCAATATTATTGGTTTGCGCTAATAAAATGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATCGGGTAAAGGCATTAGCCCGACGAATACGTCgg                                                                                                                                          >  1:58860/1‑251 (MQ=255)                                                                                              atGGATTTTTTCTGCCGCCCGGGCAATATTATTGGTTTGCGCTAATAAAATGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATCGGGTAAAGGCATTAGCCCGTCGAATACGTCGAGCTACaa                                                                                                                                   <  2:2263/250‑1 (MQ=255)                                                                                                                  gggCAATATTATTGGTTTGCGCTAATAAAATGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCAGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAACCCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCCATATCGGGTAAAGGCATTAGCCCGACGAATACGTCGGGCTACAAATATTATTGTGCTGCAggagt                                                                                                              >  1:190545/1‑248 (MQ=255)                                                                                                                            attGGTTTGCGCTAATAAAATGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATCGGGTAAAGGCATTAGCCCGACGAATACGTCGGGCTACAAATATTATTGTGCTGCAGGTGTTTTAGCGGgt                                                                                                    >  1:254781/1‑251 (MQ=255)                                                                                                                                ccgagctcTAATAAAATGAAATTGCGCAGCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCAGCCTTGTCCGCTTAACCGTTTCAGTCAGCCGAACCTGTATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAATAGGAGGCAAGATCGGGTAAAGTCATTATCCCGACGAATACGGCGGGCTACAAATATTATTGTGCTGCAGGTGTTTTAGCGGgttgtt                                                                                                <  2:282199/244‑1 (MQ=255)                                                                                                                                 tttGCGCTAATAAAATGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATCGGGTAAAGGCATTAGCCCGACGAATACGTCGGGCTACAAATATTATTGTGCTGCAGGTGTTTTAGCGGGttgttg                                                                                               >  1:92918/1‑251 (MQ=255)                                                                                                                                       cTAATAAAATGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATACCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGCAACCGCGAGCAAAGATAGGCGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATCGGGTAAAGGCATTAGCCAGACGAATACGTCGGGCTACAAATATTATTGTGCTGCAGGTGTTTTAGCGGgttgtt                                                                                                >  1:282199/1‑244 (MQ=255)                                                                                                                                            aaaaTGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACAGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGCGGCAATATCGGGTAAAGGCATTAGCCCGACGAATACGTCGGGCTACAAATATTATTGTGCTGCAGGTGTTTTAGCGGGTTGTTGATCCACAGGtt                                                                                    >  1:174277/1‑251 (MQ=255)                                                                                                                                            aaaaTGAAATTGCGCATATTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATCGGGTAAAGGCATTAGCCCGCCGAATACGTCGGGCTACAAATATTATTGAGCTGCAGGTGTTTTAGCGGGTTGTTGATCCACAGGtt                                                                                    >  2:346965/1‑251 (MQ=255)                                                                                                                                               aTGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATCGGGTAAAGGCATTAGCCCGACGAATACGTCGGGCTACAAATATTATTGTGCTGCAGGTGTTTTAGCGGGTTGTTGATCCACAGGTTCt                                                                                  >  1:232774/1‑250 (MQ=255)                                                                                                                                                                    gAAATAAAACTGTCCATCCCCGTCCCCCGCATCCTTGTCCGCTTACCCGATTCAGTCAGCCTACCCTTGATGAAACCGCGCGCCAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATAGGGTAAAGGCATTAGCCCGCCGAATAAGTCGGGCTAACAATATTATTGTGCTGCAGGCGTTTTAGCGGGTTGTTGATCAACAGGTTCTAACTGGAAGACCACATCGACCt                                                            >  2:35828/1‑251 (MQ=255)                                                                                                                                                                          aaaaTGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGATTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATCGGGTAAAGGCATTAGCCCGACGAATACGTCGGGCTACAAATATTATTGTGCTGCAGGTGTTTTAGCGGGTTGTTGATCCACAGGTTCTAACTGGAAGACCACATCGACCTGatcat                                                      >  2:126029/1‑251 (MQ=255)                                                                                                                                                                           aaaTGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAAACGCGAGCAACGATAGGTGATTACGTCATGGTTTTACAGACAATTACAGAAAAAGGAGGCAATATCGGGTAACGGCATTAGCCCGAAGAATACGTCGGGCTACAAATATTATTGTGCTGCAGGAGTTTTAGCGGGTTGTTGATCCACAGGTTCTAAATGGAAGAACACATCGACATGatcatc                                                     >  1:190259/1‑251 (MQ=255)                                                                                                                                                                           aaaTGCCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAAACGAGAGCAAAGATAGGTGATTACGTCATGGTGTTACAGCAAATTCCCGACTAAGGAGGCACTATCGGGTAACGGCATTAGCCCGACGAATACGTCGGGCTACAAATATTATTGTGCTGCTGGAGTTTTAGCGGGTTGTTGATACACAGGATCTAACTGGAAGACCACATCGACCTGatcatc                                                     >  1:238824/1‑251 (MQ=255)                                                                                                                                                                            aaTGTCCATCCCCCTCCCCCGCATCCTTGGCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATCGGGTAAAGGCATTAGCCCGACGAATACGTCGGGCTACAAATATTATTGTGCTGCAGGTGTTTTAGCGGGTTGTTGATCCACAGGTTCTAACTGGAAGACCACATCGACCTGAtcatca                                                    <  2:103753/251‑1 (MQ=255)                                                                                                                                                                                tCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATCGGGTAAAGGCATTAGCCCGACGAATACGTCGGGCTACAAATATTATTGTGCTGCAGGTGTTTTAGCGGGTTGTTGATCCACAGGTTCTAACTGGAAGACCACATCGACCTGATCATCAAACt                                                >  1:244719/1‑251 (MQ=255)                                                                                                                                                                                tCCATCCCCCTCCCCCGCATCCTTGTCAGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGACATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATCGGGTAAAGGCATTAGCCCGACGAATACGTCGGGCTACAAATATTATTGTGCTGCAGGTGTTTTAGCGGGTTGTTGATCCACAGGTTCTAACTGGAAGACCACATCGACCTGATCATCAAACt                                                >  2:251901/1‑251 (MQ=255)                                                                                                                                                                                            cccagCATCCCTGTCAGCTTAACCGTTTCAGAAAGCCTAACCTTGATGCAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTCCAGACAATTACAGAAAAAGGCGGCAATATCGGGTACAGGCATTAGCCCGACGAATACGTCGGGCTACAAATATTATTGTGCTGCAGGTGTTTTAGCGGGTTGTTGATCCACAGGTTCTAACTGGCCGACCACATCGACCTGATCATCAAACTGactaacgtcct                                    >  2:262571/5‑241 (MQ=255)                                                                                                                                                                                                      ttGTCCGCTTAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATCGGGTAAAGGCATTAGCCCGACGAATACGTCGGGCTACAAATATTATTGTGCTGCAGGTGTTTTAGCGGGTTGTTGATCCACAGGTTCTAACTGGAAGACCACATCGACCTGATCATCAAACTGAATAGCGGCCTGCTCGTAAGt                          >  1:259084/1‑251 (MQ=255)                                                                                                                                                                                                               tAACCGTTTCAGTCAGCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATCGGGTAAAGGCATTAGCCCGACGAATACGTCGGGCTACAAATATTATTGTGCTGCAGGTGTTTTAGCGGGTTGTTGATCCACAGGTTCTAACTGGAAGATCACATCGACCTGATCATCAAACTGAATAGCGGCCTGCTCGTAAGTTTCCTgg                   <  1:187023/249‑1 (MQ=255)                                                                                                                                                                                                                              gCCTAACCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATCGGGTAAAGGCATTAGCCCGACGAATACGTCGGGCTACAAATATTATTGTGCTGCAGGTGTTTTAGCGGGTTGTTGATCCACAGGTTCTAACTGGAAGACCACATCGACCTGATCATCAAACTGAATAGCGGCCTGCTCGTAAGTGTCCTGGGCGGACACCGGCGCGGc  <  2:58860/251‑1 (MQ=255)                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                      GAGGCTGATATTATTATCTTTGCGGGTAAATAGCGTATAGCCAATTTGTTCTTCCAGCGCGGCAATGCTTTTACCAAATGGCGAAGCCGTCATATGGATTTTTTCTGCCGCCCGGGCAATATTATTGGTTTGCGCTAATAAAATGAAATTGCGCATCTTTTTCGAAATAAAAATGTCCATCCCCCTCCCCCGCATCCTTGTCCGCTTAACCGTTTCAGTCAGCCTATCCTTGATGAAACCGCGAGCAAAGATAGGTGATTACGTCATGGTTTTACAGAAAATTACAGAAAAAGGAGGCAATATCGGGTAAAGGCATTAGCCCGACGAATACGTCGGGCTACAAATATTATTGTGCTGCAGGTGTTTTAGCGGGTTGTTGATCCACAGGTTCTAACTGGAAGACCACATCGACCTGATCATCAAACTGAATAGCGGCCTGCTCGTAAGTTTCCTGGGCGGACACCGGCGCGGC  >  NC_000913/3066994‑3067465

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑