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
A2 F17 I0 R1 71 95.7 2922988 91.7% 2680379 65.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 332,361 G→A 100% L269L (CTG→TTG)  fsr ← predicted fosmidomycin efflux system

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE332,3610GA81.5% 219.7 / 41.6 92L269L (CTG→TTG) fsrpredicted fosmidomycin efflux system
Reads supporting (aligned to +/- strand):  ref base G (2/15);  new base A (0/75);  total (2/90)
Fisher's exact test for biased strand distribution p-value = 3.25e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CCTACAGGCCCGCCGATCACCGTACCTGCCGCAACGGCAAACAGGAAGGCAAACAGATGAAGCTGAGCATTCTGGATAGATAATCCGAATTTTTGCATCAGATAAAAGGTGTAATAGCTGCT  >  minE/332306‑332427
                                                       |                                                                  
ccTACAGGCCCGCCGATCACCGTACCTGCCGCAACGGCAAACAGGAAGGCAAACAGATGAAGCTGAGCAtt                                                     >  1:2436621/1‑71 (MQ=255)
ccTACAGGCCCGCCGATCACCGTACCTGCCGCAACGGCAAACAGGAAGGCAAACAGATGAAGCTGAGCAt                                                      >  1:375263/1‑70 (MQ=255)
                      tACCTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAtttt                               <  1:1461677/71‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:777277/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2874339/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:687879/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2789706/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2584489/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2508697/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2505648/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:70600/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2503684/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2884763/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:844450/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2411153/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2405397/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2339207/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2323989/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2320950/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2287876/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2278929/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:429231/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:646033/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:627059/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:618684/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:606234/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:603006/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:58458/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:52923/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:512466/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2878085/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:393359/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:34653/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:314809/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:299184/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2918174/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2917123/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:684559/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2230067/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1413707/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:86448/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1647487/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1632933/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:925102/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1588620/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:934715/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:149838/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1429229/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1649966/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1335781/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1238031/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1236280/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:951836/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1227653/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1204001/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:958962/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1018594/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:84639/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1743321/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1749965/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1813007/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1881144/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1885036/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2080866/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1889186/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1740929/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2066228/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:2010887/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1925440/70‑1 (MQ=255)
                        ccTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTCGATAGATAATCCGAAttttt                              <  1:209451/70‑1 (MQ=255)
                        ccTGCCACAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1299931/70‑1 (MQ=255)
                         cTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1909644/69‑1 (MQ=255)
                         cTGCCGCAACGGCAAACAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1307956/69‑1 (MQ=255)
                                        aCAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:84858/54‑1 (MQ=255)
                                        aCAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1862299/54‑1 (MQ=255)
                                         cAGGAAGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCTAAttttt                              <  1:730189/53‑1 (MQ=255)
                                              aGGCAAACAAATGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:1037107/48‑1 (MQ=255)
                                                 caaacaaaTGAAGCTGAGCATTCTGGATAGATAATCCGAAttttt                              <  1:970084/45‑1 (MQ=255)
                                                   aaCAGATGTAGCTGAGCATTCTGGATAGATAATCCGAATTTTTGCATCAGATAAATGGTGTAATAgctgct  <  1:80069/71‑1 (MQ=255)
                                                   aaCAGATGAAGCTGAGCATTCTGGATAGATAATCCGAATTTTTGCATCAGATAAAAGGTGTAATAgctgct  <  1:289339/71‑1 (MQ=255)
                                                   aaCAGATGAAGCTGAGCATTCTGGATAGATAATCCGAATTTTTGCATCAGATAAAAGGTGTAATAgctgct  <  1:2503809/71‑1 (MQ=255)
                                                   aaCAGATGAAGCTGAGCATTCTGGATAGATAATCCGAATTTTTGCATCAGATAAAAGGTGTAATAgctgct  <  1:711445/71‑1 (MQ=255)
                                                   aaCAGATGAAGCTGAGCATTCTGGATAGATAATCCGAATTTTTGCATCAGATAAAAGGTGTAATAgctgct  <  1:2495026/71‑1 (MQ=255)
                                                   aaCAGATGAAGCTGAGCATTCTGGATAGATAATCCGAATTTTTGCATCAGATAAAAGGTGTAATAgctgct  <  1:2488391/71‑1 (MQ=255)
                                                   aaCAGATGAAGCTGAGCATTCTGGATAGATAATCCGAATTTTTGCATCAGATAAAAGGTGTAATAgctgct  <  1:2481235/71‑1 (MQ=255)
                                                   aaCAGATGAAGCTGAGCATTCTGGATAGATAATCCGAATTTTTGCATCAGATAAAAGGTGTAATAgctgct  <  1:2144842/71‑1 (MQ=255)
                                                   aaCAGATGAAGCTGAGCATTCTGGATAGATAATCCGAATTTTTGCATCAGATAAAAGGTGTAATAgctgct  <  1:1912857/71‑1 (MQ=255)
                                                   aaCAGATGAAGCTGAGCATTCTGGATAGATAATCCGAATTTTTGCATCAGATAAAAGGTGTAATAgctgct  <  1:1719689/71‑1 (MQ=255)
                                                   aaCAGATGAAGCTGAGCATTCTGGATAGATAATCCGAATTTTTGCATCAGATAAAAGGTGTAATAgctgct  <  1:1627745/71‑1 (MQ=255)
                                                   aaCAGATGAAGCTGAGCATTCTGGATAGATAATCCGAATTTTTGCATCAGATAAAAGGTGTAATAgctgct  <  1:1537684/71‑1 (MQ=255)
                                                   aaCAGATGAAGCTGAGCATTCTGGATAGATAATCCGAATTTTTGCATCAGATAAAAGGTGTAATAgctgct  <  1:1231284/71‑1 (MQ=255)
                                                   aaCAGATGAAGCTGAGCATTCTGGATAGATAATCCGAATTTTTGCATCAGATAAAAGGTGTAATAgctgct  <  1:1108861/71‑1 (MQ=255)
                                                   aaCAGATGAAGCTCAGCATTCTGGATAGATAATCCGAATTTTTGCATCAGATAAAAGGTGTAATAgctgct  <  1:2871765/71‑1 (MQ=255)
                                                       |                                                                  
CCTACAGGCCCGCCGATCACCGTACCTGCCGCAACGGCAAACAGGAAGGCAAACAGATGAAGCTGAGCATTCTGGATAGATAATCCGAATTTTTGCATCAGATAAAAGGTGTAATAGCTGCT  >  minE/332306‑332427

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A