Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A1 F17 I0 R2	276	45.3	3729697	93.0%	3468618	60.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	3,347,872	C→T	24.5%	R18W (CGG→TGG)	npr →	phosphohistidinoprotein‑hexose phosphotransferase component of N‑regulated PTS system (Npr)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,347,872	0	C	T	24.5%	91.6 / 26.5	49	R18W (CGG→TGG)	npr	phosphohistidinoprotein‑hexose phosphotransferase component of N‑regulated PTS system (Npr)
Reads supporting (aligned to +/- strand): ref base C (16/20); new base T (6/6); total (23/26)
Fisher's exact test for biased strand distribution p-value = 7.51e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGTTTTGACGCTGAAGTGCTCTTACGTAATGACG  >  W3110S.gb/3347805‑3347938

tGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCg                                                                   <  1:568186/69‑1 (MQ=255)

tGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCg                                                                   <  1:544015/69‑1 (MQ=255)

tGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCg                                                                   <  1:3423923/69‑1 (MQ=255)

tGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCg                                                                   <  1:3171740/69‑1 (MQ=255)

tGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCg                                                                   <  1:290875/69‑1 (MQ=255)

tGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCg                                                                   <  1:2715935/69‑1 (MQ=255)

tGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCg                                                                   <  1:2487460/69‑1 (MQ=255)

                 tGACCGACAAGCAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGt                                                  >  1:8274/1‑69 (MQ=255)

                   aCCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCTGGCCTGCAATGAAGCTGtt                                                 >  1:1901827/1‑68 (MQ=255)

                   aCCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCTGGCCTGCAATGAAGCTGtt                                                 >  1:1911097/1‑68 (MQ=255)

                     cGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTg                                               <  1:2481805/68‑1 (MQ=255)

                        cAAGCAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAAtt                                           >  1:2134485/1‑69 (MQ=255)

                        cAAGCAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAAtt                                           <  1:2352265/69‑1 (MQ=255)

                           gCAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTg                                               <  1:2989691/62‑1 (MQ=255)

                            cAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATg                                                         <  1:235488/51‑1 (MQ=255)

                            cAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATg                                                         <  1:2382012/51‑1 (MQ=255)

                            cAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATg                                                         <  1:1432182/51‑1 (MQ=255)

                            cAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAATTaa                                         >  1:181014/1‑67 (MQ=255)

                            cAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAATTaa                                         >  1:3550191/1‑67 (MQ=255)

                            cAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAATTaa                                         >  1:3331482/1‑67 (MQ=255)

                            cAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAATTaa                                         >  1:2219703/1‑67 (MQ=255)

                              aaCTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAATTAATGCa                                     >  1:1872761/1‑69 (MQ=255)

                                  gTTGAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGt                                 >  1:2914001/1‑69 (MQ=255)

                                     gAAATCACAAACAAGCTGGGCATGCATGCCTGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGtttt                              <  1:2910037/69‑1 (MQ=255)

                                     gAAATCACAAACAAGCTGGGCATGCATGCCTGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGtttt                              <  1:2278851/69‑1 (MQ=255)

                                     gAAATCACAAACAAGCTGGGCATGCATGCCCGTCCTGCAATGAAGCTGTTTGAATTAATGCAGGGtttt                              <  1:822848/69‑1 (MQ=255)

                                     gAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGtttt                              <  1:1079918/69‑1 (MQ=255)

                                     gAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGtttt                              <  1:1225785/69‑1 (MQ=255)

                                     gAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGtttt                              <  1:857969/69‑1 (MQ=255)

                                     gAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGtttt                              <  1:2042845/69‑1 (MQ=255)

                                          cacaAACAAGCTGGGCATGCATGCCTGGCCTGCAAt                                                          <  1:2081024/36‑1 (MQ=255)

                                          cacaAACAAGCTGGGCATGCATGCCTGGCCTGCAAt                                                          <  1:3394205/36‑1 (MQ=255)

                                           acaaacaaGCTGGGCATGCATGCCTGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGTTTTGACGc                         >  1:385928/1‑68 (MQ=255)

                                           acaaacaaGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGTTTTGACGCt                        <  1:3713271/69‑1 (MQ=255)

                                              aacaaGCTGGGCATGCATGCCTGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGTTTTGACGCTg                       <  1:1379773/67‑1 (MQ=255)

                                                 aaGCTGGGGATGCATGCCCGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGTTTTGACGCTGAAGTg                  >  1:3400252/1‑69 (MQ=255)

                                                 aaGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGTTTTGACGCTGAAGTg                  >  1:2004324/1‑69 (MQ=255)

                                                 aaGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGTTTTGACGCTGAAGTg                  >  1:796442/1‑69 (MQ=255)

                                                  aGCTGGGCATGCATGCCTGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGTTTTGACGCTg                       >  1:1363633/1‑63 (MQ=255)

                                                  aGCTGGGCATGCATGCCTGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGTTTTGACGCTg                       >  1:1164161/1‑63 (MQ=255)

                                                   gCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTg                                               <  1:717277/38‑1 (MQ=255)

                                                     tGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAAtt                                           >  1:3295633/1‑40 (MQ=255)

                                                     tGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAAtt                                           >  1:1670849/1‑40 (MQ=255)

                                                            gcatgcCCGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGtttt                              >  1:1312775/1‑46 (MQ=255)

                                                            gcatgcCCGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGtttt                              >  1:3100618/1‑46 (MQ=255)

                                                            gcatgcCCGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGtttt                              >  1:54204/1‑46 (MQ=255)

                                                            gcatgcCAGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGtttt                              >  1:1158165/1‑46 (MQ=255)

                                                             catgcCTGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGtttt                              >  1:657374/1‑45 (MQ=255)

                                                             catgcCTGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGTTTTGACGCTGAAGTGCTCTTACGTAAt      <  1:2842280/69‑1 (MQ=255)

                                                                 cccGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGtttt                              >  1:2796282/1‑41 (MQ=255)

                                                                 cccGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGTTTTGACGCTGAAGTGCTCTTACGTAATGa    >  1:929255/1‑67 (MQ=255)

                                                                 cccGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGGTTTGACGCTGAAGTGCTCTTACGTAATGACg  <  1:254330/69‑1 (MQ=255)

TGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGGCATGCATGCCCGGCCTGCAATGAAGCTGTTTGAATTAATGCAGGGTTTTGACGCTGAAGTGCTCTTACGTAATGACG  >  W3110S.gb/3347805‑3347938

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A