Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,130,258	C→G	8.9%	L647F (TTG→TTC)	fimD ←	type I pili subunit FimD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,130,258	0	C	G	8.9%	133.0 / 4.3	45	L647F (TTG→TTC)	fimD	type I pili subunit FimD
Reads supporting (aligned to +/- strand):  ref base C (19/22);  new base G (2/2);  total (21/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.71e-01

AACCGCGTGAATTGGTGCGCGTACCCGTTGCGTTTTGCAGGCCCACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCTCAGCGCGCGCGCGCTG  >  NC_002947/2130113‑2130405                                                                                                                                                  |                                                                                                                                                     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                                                                                                        <  2:332480/149‑1 (MQ=255)                                           ccACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTc                                                                                                        <  6:272577/149‑1 (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                            >  3:282964/1‑149 (MQ=255)                                                                                                                       aTGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTgg                            >  8:125264/1‑149 (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)                                                                                                                                              taTTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCTCAgcgcgcgcgcg     <  6:163220/148‑1 (MQ=255)                                                                                                                                                 tCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCTCAGCGCGCGCGCGCTg  >  1:161322/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                     AACCGCGTGAATTGGTGCGCGTACCCGTTGCGTTTTGCAGGCCCACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCTCAGCGCGCGCGCGCTG  >  NC_002947/2130113‑2130405

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: ‑