Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,130,253	G→T	9.1%	A649D (GCC→GAC)	fimD ←	type I pili subunit FimD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,130,253	0	G	T	9.1%	130.1 / 3.5	44	A649D (GCC→GAC)	fimD	type I pili subunit FimD
Reads supporting (aligned to +/- strand):  ref base G (19/21);  new base T (2/2);  total (21/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.30e-01

GCATAACCGCGTGAATTGGTGCGCGTACCCGTTGCGTTTTGCAGGCCCACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCTCA  >  NC_002947/2130109‑2130391                                                                                                                                                 |                                                                                                                                            gCATAACCGCGTGAATTGGTGCGCGTACCCGTTGCGTTTTGCAGGCCCACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCAtt                                                                                                                                         >  7:313939/1‑149 (MQ=255)     aaCCGCGTGAATTGGTGCGCGTACCCGTTGCGTTTTGCAGGCCCACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAAt                                                                                                                                     >  7:42061/1‑149 (MQ=255)      aCCGCGTGAATTGGTGCGCGTACCCGTTGCGTTTTGCAGGCCCACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAAt                                                                                                                                     <  7:2572/148‑1 (MQ=255)                   gTGCGCGTAGCCGTTGCGTTTTTGAGGCGAACATTGGCCAGGTCTGTGACTTTTATCAAGGCAGTTGTATCTCCCAGGTATCGGCCGAACTCCAGACCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTa                                                                                                                      <  4:45010/149‑1 (MQ=255)                    tGCGCGTACCCGTTGCGTTTTGCAGGCCCACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCAGC‑CTGTCATTGAATGCCAGTGGTGCGGtgc                                                                                                                     <  5:233003/149‑3 (MQ=38)                    tGCGCGTACCCGTTGCGTTTTGCAGGCCCACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAg                                                                                                                     <  6:354356/149‑1 (MQ=255)                     gcgcGTACCCGTTGCGTTTTGCAGGCCCACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACAGGCATTCAATGACAG‑GCTGCGGTAGt                                                                                                                    >  6:196278/1‑149 (MQ=255)                      cgcgTACCCGTTGCGTTTTGCAGGCCCACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGtt                                                                                                                   <  5:196278/149‑1 (MQ=255)                          tACCAGTTGCGTTTTGCAGGCCCACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCATCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCg                                                                                                               <  6:130350/149‑1 (MQ=255)                            cccGTTGCGTTTTGCAGGCCCACATTGGCCACGCCAGGGACTTCGATCCAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCAGCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCgg                                                                                                              <  2:163753/148‑1 (MQ=255)                               gTTGCGTTTTGCAGGCCCACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTc                                                                                                          >  5:272577/1‑149 (MQ=255)                                ttGCGTTTTGCAGGCCCACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGTCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCg                                                                                                         <  5:240566/149‑1 (MQ=255)                                  tcGTTTTGCAGGCCCACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCgg                                                                                                        <  8:118339/147‑1 (MQ=255)                                          cAGGCCCACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAg                                                                                               <  8:313939/149‑1 (MQ=255)                                               ccACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTc                                                                                                          >  6:236043/1‑133 (MQ=255)                                               ccACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTc                                                                                          <  6:272577/149‑1 (MQ=255)                                               ccACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTc                                                                                          <  2:332480/149‑1 (MQ=255)                                                   aTTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACg                                                                                       >  6:66663/1‑148 (MQ=255)                                                         cACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCa                                                                                 >  4:158743/1‑148 (MQ=255)                                                             ccAGGGACTTCGATCAAGGCCGCTGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAggg                                                                            <  5:66663/149‑1 (MQ=255)                                                              cAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCa                                                                                             >  8:71577/1‑131 (MQ=255)                                                              cAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCa                                                                                             <  7:71577/131‑1 (MQ=255)                                                              cAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAgggg                                                                           >  3:67527/1‑149 (MQ=255)                                                                     ttCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGAt                                                                    >  8:205027/1‑149 (MQ=255)                                                                                 cgcgGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACa                                                        <  8:42061/149‑1 (MQ=255)                                                                                               ggTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTg                                          >  8:182789/1‑149 (MQ=255)                                                                                                     ggCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCg                                    >  8:280013/1‑149 (MQ=255)                                                                                                          aaCTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTc                               <  7:280013/149‑1 (MQ=255)                                                                                                             tCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGt                             >  8:210610/1‑148 (MQ=255)                                                                                                               cAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTc                            <  3:158743/147‑1 (MQ=255)                                                                                                                     gTCAGCATGCAGCAGCACCGCACCACTGGTATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCt                      >  5:163220/1‑147 (MQ=255)                                                                                                                     gTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCt                      >  3:337810/1‑147 (MQ=255)                                                                                                                     gTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGGCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCa                    <  7:54249/149‑1 (MQ=255)                                                                                                                          cATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTg               <  7:182789/149‑1 (MQ=255)                                                                                                                           aTGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTgg              >  8:125264/1‑149 (MQ=255)                                                                                                                           aTGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTgg              >  3:282964/1‑149 (MQ=255)                                                                                                                            tGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCAGTCTTGCGGTCGTGTTCGTCACGGCTCAGGCTgtt             >  3:190645/1‑147 (MQ=255)                                                                                                                                gcagcaCCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTg         <  3:216909/149‑1 (MQ=255)                                                                                                                                 cagcaCCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGt        <  7:210610/149‑1 (MQ=255)                                                                                                                                     accgcaccACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCTGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCt    >  6:22476/1‑149 (MQ=255)                                                                                                                                       cgcaccACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCTCa  <  4:67527/149‑1 (MQ=255)                                                                                                                                       ccgcagccTGTCATTGAATGCCAGTGGTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCt    >  3:254410/8‑148 (MQ=255)                                                                                                                                       ccgcagccTGTCATTGAATGCCAGTGGTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCt    >  6:346409/8‑148 (MQ=255)                                                                                                                                       ccgcagccTGTCATTGAATGCCAGTGGTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCt    <  5:346409/141‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                            GCATAACCGCGTGAATTGGTGCGCGTACCCGTTGCGTTTTGCAGGCCCACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCTCA  >  NC_002947/2130109‑2130391

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: ‑