Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,978,320	T→C	10.0%	K94E (AAG→GAG)	flgH ←	flagellar L‑ring protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,978,320	0	T	C	10.0%	105.8 / 2.8	40	K94E (AAG→GAG)	flgH	flagellar L‑ring protein
Reads supporting (aligned to +/- strand):  ref base T (20/16);  new base C (2/2);  total (22/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

TGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGCCTTGCGGTCGCTGTACAGGTTCTGCTCGAAACCGGCCTGGTAGATCGAACCGTTGTT  >  NC_002947/4978182‑4978467                                                                                                                                            |                                                                                                                                                     tGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑g                                                                                                                                           <  8:236216/149‑1 (MQ=255)   cccTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑gg                                                                                                                                          <  2:86552/148‑1 (MQ=255)     cTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGa                                                                                                                                       >  2:154845/1‑149 (MQ=255)          tGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGc                                                                                                                                  >  5:26301/1‑149 (MQ=255)                    gTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAGTGTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCcgcg                                                                                                                         >  1:63036/1‑149 (MQ=255)                     tCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCcgcgat                                                                                                                       <  7:169792/149‑3 (MQ=255)                     tCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGt                                                                                                                        <  5:181018/148‑1 (MQ=255)                        cccTTGGTCGCGCGATCGCTGCTATAACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTCGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCtt                                                                                                                    >  5:181558/1‑149 (MQ=255)                        cccTTGGTCGCGCGATCGCTGCTATAACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTCGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCtt                                                                                                                    >  5:177604/1‑149 (MQ=255)                        cccTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAG‑GGCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACTGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCtt                                                                                                                    <  5:162895/149‑1 (MQ=255)                                 gcgcgATCGCCGCTATAACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGa                                                                                                           >  1:17414/1‑149 (MQ=255)                                  cgcgATCGCCGCTATAACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCtt                                                                                                                    <  6:153788/139‑1 (MQ=255)                                  cgcgATCGCCGCTATAACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCtt                                                                                                                    >  5:153788/1‑139 (MQ=255)                                   gcgATCGCCGCTATAACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTg                                                                                                                                                  <  5:187592/109‑1 (MQ=255)                                   gcgATCGCCGCTATAACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTg                                                                                                                                                  >  6:187592/1‑109 (MQ=255)                                      aTCGCCGCTATAACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTgc                                                                                                      <  1:154845/149‑1 (MQ=255)                                         gccgcTATAACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCt                                                                                                   >  1:88186/1‑149 (MQ=255)                                                taACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTCGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGa                                                                                             <  6:181558/148‑1 (MQ=255)                                                taACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTCGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGa                                                                                             <  6:177604/148‑1 (MQ=255)                                                 aaCCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGc                                                                                           <  6:26301/149‑1 (MQ=255)                                                  aCCGGCCTCCAGCGAAAG‑GCCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGc                                                                                           <  6:119627/148‑1 (MQ=255)                                                         tCCAGCGAAAG‑GTCACCGACACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGACAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCgtgaaggt                                                                                   >  7:195232/1‑149 (MQ=255)                                                          ccAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCgtgatggt                                                                                   >  2:26919/1‑148 (MQ=255)                                                                          cGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTcacccacc                                                                   >  2:29891/1‑149 (MQ=255)                                                                             cACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCg                                                                 >  5:199097/1‑148 (MQ=255)                                                                                   aCGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGcc                                                          <  1:29891/149‑1 (MQ=255)                                                                                       attattGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGCCTTGc                                                      <  5:94384/149‑1 (MQ=255)                                                                                                 ttGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGCCTTGCGGTCGCTGTa                                            <  2:63036/149‑1 (MQ=255)                                                                                                    ggCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGCCTTGCGGTCGCTGTACa                                          <  6:199097/148‑1 (MQ=255)                                                                                                          cTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGCCTTGCGGTCGCTGTACAGGTTCTg                                   >  3:170647/1‑149 (MQ=255)                                                                                                           tACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGCCTTGCGGTCGCTGTACAGGTTCTGc                                  >  2:212807/1‑149 (MQ=255)                                                                                                               aaaCAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGCCTTGCGGTCGCTGTACAGGTTCTGCTCg                               >  2:31401/1‑148 (MQ=255)                                                                                                                   aGCGAAGTTAGGCCGATGTCGGTCTTGCTGGTCTTGGGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGCCTTGCGGTCGCTGTACAGGTTCTGCTCGAAAc                           >  1:48367/1‑149 (MQ=255)                                                                                                                   aGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGCCTTGCGGTCGCTGTACAGGTTCt                                    <  1:242131/139‑1 (MQ=255)                                                                                                                   aGCGAAGTAAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATATGCGAGCCAGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGAGATGGTGATGATGTCACCCACACGGAACGCATTGAGGTCGATGTAAAGGTTCt                                    >  2:242131/1‑139 (MQ=255)                                                                                                                           cAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGCCTTGCGGTCGCTGTACAGGTTCTGCTCGAAACCGGCCTgg                   >  3:46205/1‑148 (MQ=255)                                                                                                                            aGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGCCTTGCGGTCGCTGTACAGGTTCTGCTCGAAACCGGcc                      <  4:263803/144‑1 (MQ=255)                                                                                                                            aGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGCCTTGCGGTCGCTGTACAGGTTCTGCTCGAAACCGGcc                      >  3:263803/1‑144 (MQ=255)                                                                                                                                       ggTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGCCTTGCGGTCGCTGTACAGGTTCTGCTCGAAACCGGCCTGGTAGATCGAACCgt      >  1:263814/1‑149 (MQ=255)                                                                                                                                       ggTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGCCTTGCGGTCGCTGTACAGGTTCTGCTCGAAACCGGCCTGGTAGATCGAACCgt      >  8:9512/1‑149 (MQ=255)                                                                                                                                           ttGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGCCTTGCGGTCGCTGTACAGGTTCTGCTCGAAACCGGCCTGGTAGATCGAACCgttgtt  <  2:17414/149‑1 (MQ=255)                                                                                                                                           ttGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGCCTTGCGGTCGCTGTACAGGTTCTGCTCGAAACCGGCCTGGTAGATCGAACCgtt     >  2:30591/1‑146 (MQ=255)                                                                                                                                           ttGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGCCTTGCGGTCGCTGTACAGGTTCTGCTCGAAACCGGCCTGGTAGATCGAACCgtt     <  1:30591/146‑1 (MQ=255)                                                                                                                                            |                                                                                                                                                     TGCCCTGGGTGGCCTTGCTGTCGCCCTTGGTCGCGCGATCGCCGCTATAACCGGCCTCCAGCGAAAG‑GTCACCGCCACCGAACGGATTATTGGTGTTGGGCGTGCTACCAAACAGCGAAGTCAGGCCGATGTCGGTCTTGCTGGTCTT‑GGCGATCTGCGAGCCCGCGTTCTTGCTGGCGGACGTGCGCTCATTGAGCGTGATGGTGATGATGTCACCCACCCGGAACGCCTTGCGGTCGCTGTACAGGTTCTGCTCGAAACCGGCCTGGTAGATCGAACCGTTGTT  >  NC_002947/4978182‑4978467

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: ‑