Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,988,364	T→G	13.1%	intergenic (+34/+60)	ycgR → / ← PP_4398	flagellar brake protein YcgR/MFS transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,988,364	0	T	G	13.1%	116.6 / 10.2	46	intergenic (+34/+60)	ycgR/PP_4398	flagellar brake protein YcgR/MFS transporter
Reads supporting (aligned to +/- strand):  ref base T (18/22);  new base G (2/4);  total (20/26)
Fisher's exact test for biased strand distribution p-value = 6.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.01e-01

CACCTTTGCCGGCGTGCGTTTCCACAACCTGAGCGGGCAGGCGCAGCGCAAGATCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGACTTGCTGACCTCTTCAGGCGCCTGTTGCTGCGCGCCCTTCTCTTCATCCTCGGTGTCTTCAGCCGCCACCGGC  >  NC_002947/4988216‑4988505                                                                                                                                                      |                                                                                                                                              caccTTTGCCGGCGTGCGTTTCCACAACCTGAGCGGGCAGGCGCAGCGCAAGATCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACctgct                                                                                                                                               <  6:250600/149‑1 (MQ=255)     tttGCCGGCGTGCGTTTCCACAGAATGAGCGGGCAGGCGCAGCGCAAGATCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAgg                                                                                                                                           >  7:49031/1‑149 (MQ=255)         ccGGCGTGCGTTTCCACAACCTGAGCGGGCAGGCGCAGCGCAAGATCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGc                                                                                                                                       <  1:27305/149‑1 (MQ=255)             cgtgcgtTTCCACAACCTGAGCGGGCAGGCGCAGCGCAAGATCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTCAGCAGGTGGCGttt                                                                                                                                   <  8:210219/149‑1 (MQ=255)              gtgcgtTTCCACAACCTGAGCGGGCAGGCGCAGCGCAAGATCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGtttt                                                                                                                                  >  1:297974/1‑149 (MQ=255)               tgcgtTTCCACAACCTGAGCGGGCAGGCGCAGCGCAAGATCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTCAGCAGGTGGCGTTTTc                                                                                                                                 <  4:282883/149‑1 (MQ=255)               tgcgtTTCCACAACCTGAGCGGGCAGGCGCAGCGCAAGATCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTCAGCAGGTGGCGTTTTc                                                                                                                                 <  6:88252/149‑1 (MQ=255)                 cgtTTCCACAACCTGAGCGGGCAGGCGCAGCGCAAGATCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCAt                                                                                                                               <  4:233651/149‑1 (MQ=255)                   tttCCACAACCTGAGCGGGCAGGCGCAGCGCAAGATCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCAttt                                                                                                                             <  1:235996/149‑1 (MQ=255)                   tttCCACAACCTGAGCGGGCAGGCGCAGCGCAAGATCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCAttt                                                                                                                             <  2:44673/149‑1 (MQ=255)                    ttCCACAACCTGAGCGGGCAGGCGCAGCGCAAGATCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTtg                                                                                                                            >  3:142419/1‑149 (MQ=255)                      ccACAACCTGAGCGGGCAGGCGCAGCGCAAGATCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTtgt                                                                                                                           <  4:142419/148‑1 (MQ=255)                            ccTGAGCGGGCAGGCGCAGCGCAAGATCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTctg                                                                                                                    >  1:295273/1‑149 (MQ=255)                             cTGAGCGGGCAGGCGCAGCGCAAGATCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTctgc                                                                                                                   <  6:42264/149‑1 (MQ=255)                              tGAGCGGGCAGGCGCAGCGCAAGATCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTctgct                                                                                                                  >  5:60888/1‑149 (MQ=255)                                                  aaGATCGAGATTTTCGTGTACCAGCTGCAGCGTGAGGCGCTGCGGTTCGACAAGGA‑CGATTAATGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGt                                                                                              <  4:226467/149‑1 (MQ=255)                                                  aaGATCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCggg                                                                                               >  4:215281/1‑148 (MQ=255)                                                      tCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAAc                                                                                          >  7:276568/1‑149 (MQ=255)                                                         agagTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTgctgggc                                                                                                              >  7:16049/1‑126 (MQ=255)                                                         agagTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTgctgggc                                                                                                              <  8:16049/126‑1 (MQ=255)                                                          gagTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGc                                                                                      <  6:60888/149‑1 (MQ=255)                                                             tttCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACctgct                                                                                                                                               <  8:42781/89‑1 (MQ=255)                                                             tttCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACctgct                                                                                                                                               >  7:42781/1‑89 (MQ=255)                                                                   gtACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTgctgggct                                                                                                             <  5:206477/117‑1 (MQ=255)                                                                   gtACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTgctgggct                                                                                                             >  6:206477/1‑117 (MQ=255)                                                                    tACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACAcc                                                                             >  3:124605/1‑148 (MQ=255)                                                                      ccAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGAc                                                                          >  2:74064/1‑149 (MQ=255)                                                                       cAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGAGCGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGAc                                                                          >  1:215772/1‑149 (MQ=255)                                                                         gCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAACCCCGCTCCTACACCGACTTg                                                                       >  1:96758/1‑149 (MQ=255)                                                                            gCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTcgc                                                                                                  <  8:296056/119‑1 (MQ=255)                                                                               gCGTGAGGCGCGGCGGTTCGACAAAGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGACTTGCTGAcc                                                                 >  5:44683/1‑149 (MQ=255)                                                                                 gTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGACTTGCTGACctc                                                               <  8:49031/149‑1 (MQ=255)                                                                                    aGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGACTTGCTGACCTCTTc                                                            <  4:124605/149‑1 (MQ=255)                                                                                        gcggcgGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGc                                                                                      >  6:247145/1‑119 (MQ=255)                                                                                        gcggcgGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGc                                                                                      <  5:247145/119‑1 (MQ=255)                                                                                            cggTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGACTTGCTGACCTCTTCAGGCGCCt                                                    <  3:215281/149‑1 (MQ=255)                                                                                                  gACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGAGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGACTTGCTGACCTCTTCAGGCGCCTGTtgct                                              >  3:210660/1‑149 (MQ=255)                                                                                                     aaGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGATTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGACTTGCTGACCTCTTCAGGCGCCTGTTGCTgcg                                           >  2:174068/1‑149 (MQ=255)                                                                                                      aagA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGACTTGCTGACCTCTTCAGGCGCCTGTTGCTgcgc                                          <  6:44683/147‑1 (MQ=255)                                                                                                       ggA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGACTTGCTGACCTCTTCAGGCGCCTg                                                   <  8:127817/139‑1 (MQ=255)                                                                                                       ggA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGAGGGTAAACCCGCTCCTACACCGACTTGCTGACCTCTTCAGGCGCCTg                                                   >  7:127817/1‑139 (MQ=255)                                                                                                           cGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGACTTGCTGACCTCTTCAGGCGCCTGTTGCTGCGCGccc                                      <  1:74064/149‑1 (MQ=255)                                                                                                                 ttGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGACTTGCTGACCTCTTCAGGCGCCTGTTGCTGCGCGCCCTtctc                                 <  1:174068/148‑1 (MQ=255)                                                                                                                    aTCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGACTTGCTGACCTCTTCAGGCGCCTGTTGCTGCGCGCCCTTCTCTTc                              <  4:118422/148‑1 (MQ=255)                                                                                                                       gtcggtcgGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGACTTGCTGACCTCTTCAGGCGCCTGTTGCTGCGCGCCCTTCTCTTCATc                           <  2:297974/148‑1 (MQ=255)                                                                                                                          ggtcggtAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGACTTGCTGACCTCTTCAGGCGCCTGTTGCTGCGCGCCCTTCTCTTCATCCTCg                       <  8:276568/149‑1 (MQ=255)                                                                                                                                       gAAAACGCCACCTCAGCAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGCAAACCCGCTCCTACACCGACTTGCTGACCTCTTCAGGCGCCTGTTGCTGCGCGCCCTTCTCTTCATCCTCGGTGTCTTCAgccg          >  1:92744/1‑149 (MQ=255)                                                                                                                                         aaaCGCCACCTCAGCAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGACTTGCTGACCTCTTCAGGCGCCTGTTGCTGCGCGCCCTTCTCTTCATCCTCGGTGTCTTc               <  5:952/142‑1 (MQ=255)                                                                                                                                         aaaCGCCACCTCAGCAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGACTTGCTGACCTCTTCAGGCGCCTGTTGCTGCGCGCCCTTCTCTTCATCCTCGGTGTCTTc               >  6:952/1‑142 (MQ=255)                                                                                                                                               ctgctgctgATGTGTCGTTTTCATTTGTGTTTCTGCTGGGCTTGCCGCTTCGCGGGTAAACCCGCTCCTACAGCGACTTGCTGACCTCTTCAGGCGCGTGTTGCTGCGCGACCTTCTCTTCATCCTCGGTGTATTCAGCCGCCAGCgtc  <  2:96758/146‑3 (MQ=255)                                                                                                                                                      |                                                                                                                                              CACCTTTGCCGGCGTGCGTTTCCACAACCTGAGCGGGCAGGCGCAGCGCAAGATCGAGAGTTTCGTGTACCAGCTGCAGCGTGAGGCGCGGCGGTTCGACAAGGA‑CGATTATTGATCGTCGGTCGGTAAAACAGAAAACGCCACCTGCTGAGGTGGCGTTTTCATTTGTGTTTCTGCTGGGCTGGCCGCTTCGCGGGTAAACCCGCTCCTACACCGACTTGCTGACCTCTTCAGGCGCCTGTTGCTGCGCGCCCTTCTCTTCATCCTCGGTGTCTTCAGCCGCCACCGGC  >  NC_002947/4988216‑4988505

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑