Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,966,615	T→G	9.3%	A354A (GCA→GCC)	fliD ←	flagellar filament capping protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,966,615	0	T	G	9.3%	121.9 / 4.9	43	A354A (GCA→GCC)	fliD	flagellar filament capping protein
Reads supporting (aligned to +/- strand):  ref base T (16/23);  new base G (2/2);  total (18/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.42e-01

GCTTGGTGAGCTCAGTTAGGTTGTCGTTGAGGTTCTTTGTCCGCGTTGCCAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTATTGATCCCCATCTGCGAAAGCATGGAGATGCTCCCCGCCCCGGTGCTCTTCACCAGCTCGTTACGCACTGTCGAGAC  >  NC_002947/4966473‑4966761                                                                                                                                               |                                                                                                                                                   gctTGGTGAGCTCAGTTAGGTTGTCGTTGAGGTTCTTTGTCCGCGTTGCCAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCAccc                                                                                                                                              >  5:135208/1‑149 (MQ=255)  ctTGGTGAGCTCAGTTAGGTTGTCGTTGAGGTTCTTTGTCCGCGTTGCCAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCt                                                                                                                                             <  4:87345/149‑1 (MQ=255)   ttGGTGAGCTCAGTTAGGTTGTCGTTGAGGTTCTTTGTCCGCGTTGCCAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCtt                                                                                                                                            >  2:129993/1‑149 (MQ=255)      gTGAGCTCAGTTAGGTTGTCGTTGAGGTTCTTTGTCCGCGTTGCCAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTgg                                                                                                                                          <  1:114423/148‑1 (MQ=255)      gTGAGCTCAGTTAGGTTGTCGTTGAGGTTCTTTGTCCGCGTTGCCAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTgg                                                                                                                                          >  8:138533/1‑148 (MQ=255)      gTGAGCTCAGTTAGGTTGTCGTTGAGGTTCTTTGTCCGCGTTGCCAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGc                                                                                                                                         <  1:129993/149‑1 (MQ=255)      gTGAGCTCAGTTAGGTTGGCGTTGAGGTTCTTTGTCCGCGTTGCCAAGATTCCGGTCGTGCCAGAGTTATCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTgg                                                                                                                                          <  7:173530/148‑1 (MQ=255)           cTCAGTTAGGTTGTCGTTGAGGTTCTTTGTCCGCGTTGCCAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCa                                                                                                                                        <  6:213940/145‑1 (MQ=255)           cTCAGTTAGGTTGTCGTTGAGGTTCTTTGTCCGCGTTGCCAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCa                                                                                                                                        >  5:213940/1‑145 (MQ=255)              aGTTAGGTTGTCGTTGAGGTTCTTTGTCCGCGTTGCCAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCt                                                                                                                                 >  3:246271/1‑149 (MQ=255)                  aGGTTGTCGTTGAGGTTCTTTGTCCGCGTTGCCAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGt                                                                                                                              <  4:48082/148‑1 (MQ=255)                              aGGTTCTTTGTCAGCGTTGCCAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCGGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCGTTGTCCCACTTGGTATc                                                                                                                 <  2:9067/149‑1 (MQ=255)                                 ttCTTTGTCCGCGTTGCCAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTc                                                                                                              >  3:106145/1‑149 (MQ=255)                                   cTTTGTCCGCGTTGCCAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTc                                                                                                              >  4:68823/1‑147 (MQ=255)                                       gTCCGCGTTGCCAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCa                                                                                                         <  6:154224/148‑1 (MQ=255)                                           gcgTTGCCAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAAc                                                                                                    <  3:68823/149‑1 (MQ=255)                                              ttGCCAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCGTTGGCAACAGCCTTGTCCCACTTGGTTTCGTCCAGCACCAACAgg                                                                                                 <  4:110148/149‑1 (MQ=255)                                                  cAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCg                                                                                             >  7:30056/1‑149 (MQ=255)                                                    aGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTc                                                                                           <  5:229748/149‑1 (MQ=255)                                                       ttCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTctgc                                                                                        <  4:246271/149‑1 (MQ=255)                                                                  ccAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTAt                                                                              <  2:65229/148‑1 (MQ=255)                                                                       gtAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTGTGCTGATCGGTATTGATcc                                                                        >  3:173880/1‑149 (MQ=255)                                                                        tAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTATTGATccc                                                                       >  8:45346/1‑149 (MQ=255)                                                                                  tGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGc                                                                                                <  7:205956/114‑1 (MQ=255)                                                                                  tGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGc                                                                                                >  8:205956/1‑114 (MQ=255)                                                                                      cGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCGGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTATTGATCCCCATCTGCGAAAGCa                                                         >  1:42802/1‑149 (MQ=255)                                                                                      cGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCGGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTATTGATCCCCATCTGCGAAAGCa                                                         >  1:38898/1‑149 (MQ=255)                                                                                        cAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTATTGATCCCCATCTGCGAAAGCATg                                                       <  4:106145/149‑1 (MQ=255)                                                                                             aTGCGCTTGATCAGGCCCTTGTCACCGGTGAACCCCGCCGCGATATCGGCTGCCCCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGAGCGGTATTGATCCCCCTCTGCGAAAGCATGgagct                                                  >  8:187721/1‑147 (MQ=255)                                                                                                   ttGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTATTGATCCCCATCTGCGAAAGCATGGAGATGCTccc                                            >  5:167935/1‑149 (MQ=255)                                                                                                         aGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTATTGATCCCCATCTGCGAAAGCATGGAGATGCTccccgcccc                                      >  2:90184/1‑149 (MQ=255)                                                                                                         aGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTATTGATCCCCATCTGCGAAAGCATGGAGATGCTccccgccc                                       <  7:45346/148‑1 (MQ=255)                                                                                                          ggCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTATTGATCCCCATCTGCGAAAGCATGGAGATGCTccccgccccg                                     <  7:187721/149‑1 (MQ=255)                                                                                                            cccTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTATTGATCCCCATCTGCGAAAGCATGGAGATGCTCCCCGCCCCGGt                                   <  6:167935/149‑1 (MQ=255)                                                                                                                 gTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTATTGATCCCCATCTGCGAAAGCATGGAGATGCTCCCCGCCCCGGTGctc                               <  6:135208/148‑1 (MQ=255)                                                                                                                     ccGGTGAACACCGCCGCGATATCGGCGGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTATTGATCCCCATCTGCGAAAGCATGGAGATGCTCCCCGCCCCGGTGCTCTTCAc                          <  2:42802/149‑1 (MQ=255)                                                                                                                     ccGGTGAACACCGCCGCGATATCGGCGGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTATTGATCCCCATCTGCGAAAGCATGGAGATGCTCCCCGCCCCGGTGCTCTTCAc                          <  2:38898/149‑1 (MQ=255)                                                                                                                        gTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTc                                                                                           >  7:97023/1‑81 (MQ=255)                                                                                                                        gTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTc                                                                                           <  8:97023/81‑1 (MQ=255)                                                                                                                                     cgATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTATTGATCCCCATCTGCGAAAGCATGGAGATGCTCCCCGCCCCGGTGCTCTTCACCAGCTCGTTACGCACt          <  1:90184/149‑1 (MQ=255)                                                                                                                                          tCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTATTGATCCCCATCTGCGAAAGCATGGAGATGCTCCCCGCCCCGGTGCTCTTCACCAGCTCGTTACGCACTGTCga     <  8:30056/149‑1 (MQ=255)                                                                                                                                            ggCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTATTGATCCCCATCTGCGAAAGCATGGAGATGCTCCCCGCCCCGGTGCTCTTCACCAGCTCGTTACGCACTGTCgaga   >  4:141708/1‑149 (MQ=255)                                                                                                                                             gCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTATTGATCCCCATCTGCGAAAGCATGGAGATGCTCCCCGCCCCGGTGCTCTTCACCAGCTCGTTACGCACTGTCGAGAc  <  7:138533/149‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                   GCTTGGTGAGCTCAGTTAGGTTGTCGTTGAGGTTCTTTGTCCGCGTTGCCAAGATTCCGGTCGTGCCAGTGTAAGCATCCGTGGCCGCAGTCATGCGCTTGATCAGGCCCTTGTCACCGGTGAACACCGCCGCGATATCGGCTGCACCCTTGGCAACAGCCTTGTCCCACTTGGTATCGTCCAGCACCAACAGGCCCGTCTGCTGATCGGTATTGATCCCCATCTGCGAAAGCATGGAGATGCTCCCCGCCCCGGTGCTCTTCACCAGCTCGTTACGCACTGTCGAGAC  >  NC_002947/4966473‑4966761

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: ‑