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
A5 F28 I3 R1 375 42.1 2927644 71.4% 2090337 57.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 3,663,305 A→G R285R (CGT→CGC)  rffG ← dTDP‑glucose 4,6‑dehydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,663,3050AG76.3% 102.4 / 29.6 59R285R (CGT→CGC) rffGdTDP‑glucose 4,6‑dehydratase
Reads supporting (aligned to +/- strand):  ref base A (14/0);  new base G (45/0);  total (59/0)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.45e-01

TAACGCAGATCATGCCCCGGACGGTCAGCGACAAAGGTGATCAGGTCACGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAG  >  W3110S.gb/3663258‑3663343
                                               |                                      
tAACGCAGATCATGCCCCGGACGGTCAGCGACAAAGGTGATCAGGTCACGATAGTGCGCCAc                          >  1:778261/1‑62 (MQ=255)
tAACGCAGATCATGCCCCGGACGGTCAGCGACAAAGGTGATCAGGTCACGATAGTGCGCCAc                          >  1:405854/1‑62 (MQ=255)
tAACGCAGATCATGCCCCGGACGGTCAGCGACAAAGGTGATCAGGTCACGATAGTGCGCCAc                          >  1:1634663/1‑62 (MQ=255)
tAACGCAGATCATGCCCCGGACGGTCAGCGACAAAGGTGATCAGGTCACGATAGTGCGCCAc                          >  1:2252018/1‑62 (MQ=255)
tAACGCAGATCATGCCCCGGACGGTCAGCGACAAAGGTGATCAGGTCACGATAGTGCGCCAc                          >  1:1498724/1‑62 (MQ=255)
tAACGCAGATCATGCCCCGGACGGTCAGCGACAAAGGTGATCAGGTCACGATAGTGCGCCAc                          >  1:2298076/1‑62 (MQ=255)
tAACGCAGATCATGCCCCGGACGGTCAGCGACAAAGGTGATCAGGTCACGATAGTGCGCCAc                          >  1:2897816/1‑62 (MQ=255)
tAACGCAGATCATGCCCCGGACGGTCAGCGACAAAGGTGATCAGGTCACGATAGTGCGCCAc                          >  1:2823862/1‑62 (MQ=255)
tAACGCAGATCATGCCCCGGACGGTCAGCGACAAAGGTGATCAGGTCACGATAGTGCGCCAc                          >  1:840790/1‑62 (MQ=255)
tAACGCAGATCATGCCCCGGACGGTCAGCGACAAAGGTGATCAGGTCACGATAGTGCGCCAc                          >  1:130971/1‑62 (MQ=255)
tAACGCAGATCATGCCCCGGACGGTCAGCGACAAAGGTGATCAGGTCACGATAGTGCGCCAc                          >  1:1297464/1‑62 (MQ=255)
tAACGCAGATCATGCCCCGGACGGTCAGCGACAAAGGTGATCAGGTCACGATAGTGCGCCAc                          >  1:1231375/1‑62 (MQ=255)
tAACGCAGATCATGCCCCGGACGGTCAGCGACAAAGGTGATCAGGTCACGATAGTGCGCCAc                          >  1:2805241/1‑62 (MQ=255)
tAACGCAGATCATGCCCCGGACGGTCAGCGACAAAGGTGATCAGGTCACGATAGTGCGCCAc                          >  1:2659945/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCa   >  1:1682773/1‑61 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCa   >  1:2578343/1‑61 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCa   >  1:2166954/1‑61 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCa   >  1:373040/1‑61 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCa   >  1:2752364/1‑61 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCa   >  1:1072653/1‑61 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCa   >  1:942851/1‑61 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCa   >  1:776069/1‑61 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCa   >  1:1522298/1‑61 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCa   >  1:446584/1‑61 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:633696/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:957849/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:951936/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:2835079/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:69187/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:2905042/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:619192/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:368802/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:484361/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:373359/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:405043/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:2389950/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:1934891/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:1055201/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:1077092/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:1119705/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:1348633/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:1350240/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:1396842/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:1408388/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:1480753/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:1614938/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:1626093/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:1809226/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:2652240/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:1985434/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:2069224/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:2080790/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:2118259/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:235310/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:1053450/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:2433152/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:2448841/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:2462304/1‑62 (MQ=255)
                        tCAGCGACAAAGGTGATCAGATCGCGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAg  >  1:2582127/1‑62 (MQ=255)
                                               |                                      
TAACGCAGATCATGCCCCGGACGGTCAGCGACAAAGGTGATCAGGTCACGATAGTGCGCCACGCCGTGCGGCTTGTTCGGAGCCAG  >  W3110S.gb/3663258‑3663343

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