Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,789,023	C→A	12.8%	C60* (TGC→TGA) ‡	ynfM →	efflux transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,789,023	0	C	A	12.8%	99.2 / 7.7	39	C60* (TGC→TGA) ‡	ynfM	efflux transporter
Reads supporting (aligned to +/- strand):  ref base C (17/17);  new base A (2/3);  total (19/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.45e-01

AAAACTGCAGTAGCCCCCCTCCTCCTTGAGCCAAAACCTGCCATCCTGACCGAAATGTGGATCGAAAAAGGCACACCCGCCTTCATGAAAACCGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGTTCGGCCTGCTGATCACCGGCCCCATTTCTGACCGCATCGGACGCAAGCCCGT  >  NC_002947/5788880‑5789169                                                                                                                                                |                                                                                                                                                   aaaaCTGCAGTATCCCCCCTCCTCATTGAGCCAAAAGCTTCCATCCTGACCTAAATGTGGATCGAAAAAGGCACACCCGCCTTCATGAAAACCGTGATGGCCTTGTTAAGAGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTAc                                                                                                                                                <  6:2300/148‑1 (MQ=255)   aaCTGCAGTAGCCCCCCTCCTCCTTGAGCCAAAACCTGCCATCCTGACCGAAATGTGGATCGAAAAAGGCACACCCGCCTTCATGAAAACCGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACGCAGTACAg                                                                                                                                              >  4:269582/1‑148 (MQ=255)     cTGCAGTAGCCCCCCTCCTCCTTGAGCCAAAACCTGCCATCCTGACCGAAATGTGGATCGAAAAAGGCACACCCGCCTTCATGAAAACCGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACGCAGTACAGcaa                                                                                                                                           <  3:269582/149‑3 (MQ=255)        cAGTAGCCCCCCTCCTCCTTGAGCCAAAACCTGCCATCCTGACCGAAATGTGGATCGAAAAAGGCACACCCGCCTTCATGAAAACCGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCgatg                                                                                                                                        <  7:215090/149‑1 (MQ=255)        cAGTAGCCCCCCTCCTCCTTGAGCCAAAACCTGCCATCCTGACCGAAATGTGGATCGAAAAAGGCACACCCGCCTTCATGAAAACCGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACGCAGTACAGcaag                                                                                                                                          <  5:70505/147‑4 (MQ=255)        cAGTAGCCCCCCTCCTCCTTCAGCCAAAACCTGCCATCCTGACCGAAATGTGGATCGAAAAAGGCACACCCGCCTTCATGAAAACCGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACGCAGTACAGcaag                                                                                                                                          <  1:134503/147‑4 (MQ=255)          gTAGCCCCCCTCCTCCTTGAGCCAAAACCTGCCATCCTGACCGAAATGTGGATCGAAAAAGGCACACCCGCCTTCATGAAAACCGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCgatgat                                                                                                                                      <  3:141574/149‑1 (MQ=255)           tAGCCCCCCTCCTCCTTGAGCCAAAACCTGCCATCCTGACCGAAATGTGGATCGAAAAAGGCACACCCGCCTTCATGAAAACCGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGatgatg                                                                                                                                     >  3:26189/1‑149 (MQ=255)               cccccTCCTCCTTGAGCCAAAACCTGCCATCCTGACCGAAATGTGGATCGAAAAAGGCACACCCGCCTTCATGAAAACCGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCctc                                                                                                                                 <  6:87054/149‑1 (MQ=255)                   ctcctcctTGAGCCAAAACCTGCCATCCTGACCGAAATGTGGATCGAAAAAGGCACACCCGACTTCATGAAAACCGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTctgct                                                                                                                             <  4:26189/149‑1 (MQ=255)                         ctTGAGCCAAAACCTGCCATCCTGACCGAAATGTGGATCGAAAAAGGCACACCCGCCTTCATGAAAACCGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCg                                                                                                                       <  6:50446/149‑1 (MQ=255)                                                           ggATCGAAAAAGGCACACCCGCCTTCATGAAAACCGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTg                                                                                     >  7:111614/1‑149 (MQ=255)                                                             aTCGAAAAAGGCACACCCGCCTTCATGAAAACCGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGt                                                                                   >  7:275505/1‑149 (MQ=255)                                                                    aaGGCACACCCGCCTTCATGAAAACCGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCg                                                                            >  3:256091/1‑149 (MQ=255)                                                                             ccGCCTTCATGAAAACCGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCAcc                                                                   >  1:62192/1‑149 (MQ=255)                                                                                        aaaaCCGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTgg                                                         <  8:111614/148‑1 (MQ=255)                                                                                          aaCCGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGt                                                      >  6:119957/1‑149 (MQ=255)                                                                                             cGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGTTCg                                                   <  2:62192/149‑1 (MQ=255)                                                                                               tGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGTTCGGc                                                 >  5:258476/1‑149 (MQ=255)                                                                                                gCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGTTCGGcc                                                >  8:77556/1‑149 (MQ=255)                                                                                                 cTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCCTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGTTCGGcc                                                <  8:93554/148‑1 (MQ=255)                                                                                                         gTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACaga                                                                                             <  4:70203/95‑1 (MQ=255)                                                                                                         gTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACaga                                                                                             >  3:70203/1‑95 (MQ=255)                                                                                                              gcggcgGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACTCGGCACAGAGCAGCCTGGTGCTGTCGgt                                                                          >  4:294947/1‑109 (MQ=255)                                                                                                              gcggcgGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGgt                                                                          <  3:294947/109‑1 (MQ=255)                                                                                                                    gTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGTTCGGCCTGCTGATCACCGGCCCCAtt                            >  1:32660/1‑149 (MQ=255)                                                                                                                    gTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGTTCGGCCTGCTGATCACCGGCCCCAtt                            >  7:254567/1‑149 (MQ=255)                                                                                                                     tttCGCCACCTTCGCCTTGGTGTACTGCGTTCAGCCGTTGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACaga                                                                                             <  1:146803/83‑1 (MQ=255)                                                                                                                     tttCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGTTCGGCCTGCTGATCACCGGCCCCAttt                           <  4:256091/149‑1 (MQ=255)                                                                                                                     tttCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGTTCGGCCTGCTGATCACCGGCCCCAtt                            >  7:118455/1‑148 (MQ=255)                                                                                                                        cGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGTTCGGCCTGCTGATCACCGGCCCCATTTCt                         <  8:275505/148‑1 (MQ=255)                                                                                                                         gCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCAt                                                              >  6:59106/1‑110 (MQ=255)                                                                                                                               ttCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGTTCGGCCTGCTGATCACCGGCCCCATTTCTGACCGCAt                 >  4:1987/1‑149 (MQ=255)                                                                                                                                  gCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCAATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGTTCGGCctg                                              >  5:46605/1‑117 (MQ=255)                                                                                                                                  gCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCAATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGTTCGGCctg                                              <  6:46605/117‑1 (MQ=255)                                                                                                                                   ccTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGTTCGGCCTGCTGATCACCGGCCCCATTTCTGACCGCATCGGa             <  5:119957/149‑1 (MQ=255)                                                                                                                                       gCTGTACGCAGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGTTCGGCCTGCTGATCACCGGCCCCATTTCTGACCGCATCGGACGc          >  5:32718/1‑148 (MQ=255)                                                                                                                                             cTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGTTCGGCCTGCTGATCACCGGCCCCATTTCTGACCGCATCGGACGCAAGccc    <  6:258476/148‑1 (MQ=255)                                                                                                                                               gCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGTTCGGCCTGCTGATCACCGGCCCCATTTCTGACCGCATCGGACGCAAGCCCGt  >  3:3065/1‑148 (MQ=255)                                                                                                                                                |                                                                                                                                                   AAAACTGCAGTAGCCCCCCTCCTCCTTGAGCCAAAACCTGCCATCCTGACCGAAATGTGGATCGAAAAAGGCACACCCGCCTTCATGAAAACCGTGCTGGCCTTGTTCAGCGGCGGTTTCGCCACCTTCGCCTTGCTGTACTGCGTACAGCCGATGATGCCTCTGCTGTCCCGGGAGTTTGCCATCAACGCGGCACAGAGCAGCCTGGTGCTGTCGGTGTCCACCGCCATGCTGGCGTTCGGCCTGCTGATCACCGGCCCCATTTCTGACCGCATCGGACGCAAGCCCGT  >  NC_002947/5788880‑5789169

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑