BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,130,263	A→C	8.9%	S646A (TCA→GCA)	fimD ←	type I pili subunit FimD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,130,263	0	A	C	8.9%	126.0 / 4.8	45	S646A (TCA→GCA)	fimD	type I pili subunit FimD
Reads supporting (aligned to +/- strand): ref base A (20/21); new base C (2/2); total (22/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.21e-01

GTGCGCGTACCCGTTGCGTTTTGCAGGCCCACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCTCAGCGCGCGCGCGCTGTCG  >  NC_002947/2130127‑2130408

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                     >  6:346409/8‑148 (MQ=255)

                                                                                                                    ccgcagccTGTCATTGAATGCCAGTGGTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCt                     <  5:346409/141‑1 (MQ=255)

                                                                                                                    ccgcagccTGTCATTGAATGCCAGTGGTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCt                     >  3:254410/8‑148 (MQ=255)

                                                                                                                               taTTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCTCAgcgcgcgcgcg        <  6:163220/148‑1 (MQ=255)

                                                                                                                                  tCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCTCAGCGCGCGCGCGCTg     >  1:161322/1‑149 (MQ=255)

                                                                                                                                    aaTGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCTCAGCGCGCGCGCGCTGTc   >  7:132479/1‑149 (MQ=255)

                                                                                                                                     aTGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCTCAGCGCGCGCGCGCTGTCg  >  8:271445/1‑149 (MQ=255)

GTGCGCGTACCCGTTGCGTTTTGCAGGCCCACATTGGCCACGCCAGGGACTTCGATCAAGGCCGCGGTATCTCCCAGGTATCGGCCGAACTCCAGCCCGTCAGCATGCAGCAGCACCGCACCACTGGCATTCAATGACAG‑GCTGCGGTAGTTGTCGGCTTCGGTATAGCCAGCACTCACGCTGGCATAGGGGGCCTGATGGCCGAGCGACAGTGCCGCTGTCTTGCGGGCGTGTTCGTCACGGCTCAGGCTGGTGCTGTAGCTCAGCGCGCGCGCGCTGTCG  >  NC_002947/2130127‑2130408

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: `‑`