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 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 373,537 C→T 25.2% D129D (GAC→GAT)  fepE → regulator of length of O‑antigen component of lipopolysaccharide chains

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE373,5370CT25.2% 131.9 / 37.4 107D129D (GAC→GAT) fepEregulator of length of O‑antigen component of lipopolysaccharide chains
Reads supporting (aligned to +/- strand):  ref base C (55/24);  new base T (8/19);  total (64/43)
Fisher's exact test for biased strand distribution p-value = 5.00e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.98e-01

Only 100 of 107 total aligned reads displayed.

GGTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTG  >  minE/373489‑373594
                                                |                                                         
ggTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGaaaa                                        >  1:3331326/1‑68 (MQ=255)
ggTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGaaaa                                        >  1:227277/1‑68 (MQ=255)
ggTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGaaaa                                        >  1:2023772/1‑68 (MQ=255)
ggTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGaaaa                                        >  1:1844082/1‑68 (MQ=255)
  ttAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATc                                      <  1:61965/68‑1 (MQ=255)
   tAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcg                                     >  1:3363131/1‑68 (MQ=255)
   tAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcg                                     >  1:244929/1‑68 (MQ=255)
   tAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcg                                     >  1:1577565/1‑68 (MQ=255)
   tAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATc                                      >  1:1625959/1‑67 (MQ=255)
                 agTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGc                      <  1:1027761/69‑1 (MQ=255)
                 agTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGc                      <  1:79417/69‑1 (MQ=255)
                 agTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGc                      <  1:2723667/69‑1 (MQ=255)
                 agTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGc                      <  1:1107463/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTTAAAGAAGCGAAAATCGACCCACTGGATCTGCa                     <  1:2831428/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                     <  1:2757906/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                     <  1:479373/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                     <  1:2644204/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                     <  1:2769417/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                     <  1:1746939/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                     <  1:2803689/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                     <  1:469183/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                     <  1:1109901/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                     <  1:1195702/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                     <  1:1592560/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                     <  1:2345649/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                     <  1:101392/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                     <  1:831737/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                     <  1:2412929/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                     <  1:1454295/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                     <  1:839557/69‑1 (MQ=255)
                   tACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCAt                    >  1:1843938/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                 >  1:3074205/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                 >  1:334122/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                 >  1:3374615/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                 >  1:1231593/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                 >  1:2429065/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                 >  1:373533/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                 >  1:3072300/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                 >  1:546724/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                 >  1:602756/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                 <  1:1245647/54‑1 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                 >  1:1618448/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                 >  1:832966/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                 >  1:875730/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacca                                 <  1:643057/54‑3 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCAt                    >  1:2049714/1‑67 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg                  >  1:2662145/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg                  >  1:2050860/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg                  >  1:2468898/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg                  >  1:2426194/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg                  >  1:2300291/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg                  >  1:2277955/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg                  >  1:2179367/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg                  >  1:3389758/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg                  >  1:347173/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg                  >  1:1876394/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg                  >  1:1500968/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATc                   >  1:1779859/1‑68 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc               <  1:3387097/69‑1 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc               <  1:1349102/69‑1 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc               >  1:313586/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc               <  1:44285/69‑1 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc               >  1:288359/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc               >  1:484610/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc               >  1:2876191/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc               >  1:1317306/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc               >  1:1127555/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc               >  1:2685707/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc               >  1:1544905/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc               >  1:1687716/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc               <  1:1718465/69‑1 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc               <  1:2648258/69‑1 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc               <  1:2588065/69‑1 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc               >  1:2157912/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGAACAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc               >  1:1962217/1‑69 (MQ=255)
                           ttCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCa              <  1:2732224/67‑1 (MQ=255)
                           ttCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCa              <  1:3123218/67‑1 (MQ=255)
                           ttCATCACCTTATGCGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAAt            <  1:186153/69‑1 (MQ=255)
                             catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg          >  1:2840410/1‑69 (MQ=255)
                             catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg          >  1:3104746/1‑69 (MQ=255)
                             catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg          >  1:653184/1‑69 (MQ=255)
                             catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg          >  1:644937/1‑69 (MQ=255)
                             catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg          >  1:472056/1‑69 (MQ=255)
                             catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg          >  1:1923087/1‑69 (MQ=255)
                             catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg          >  1:2097096/1‑69 (MQ=255)
                             catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg          >  1:1127733/1‑69 (MQ=255)
                                caCCTTATGTGATGGATCAATTAAAAGAAGCGATAATCGACCCACTGGATCTGCa                     <  1:2664771/55‑1 (MQ=255)
                                caCCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCTCAATTGTCg       <  1:373303/69‑1 (MQ=255)
                                caCCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCg       <  1:1914623/69‑1 (MQ=255)
                                caCCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCg       <  1:1545549/69‑1 (MQ=255)
                                caCCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCg       <  1:1744742/69‑1 (MQ=255)
                                     tATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTg  >  1:537640/1‑69 (MQ=255)
                                     tATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTg  >  1:1053526/1‑69 (MQ=255)
                                     tATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTg  >  1:1297706/1‑69 (MQ=255)
                                     tATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTg  >  1:1198086/1‑69 (MQ=255)
                                     tATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTg  >  1:1508458/1‑69 (MQ=255)
                                     tATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTg  >  1:1416194/1‑69 (MQ=255)
                                     tATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTg  >  1:2145637/1‑69 (MQ=255)
                                       tgtgATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCg       <  1:784554/62‑1 (MQ=255)
                                           aTGGATCAATTAAAAGACGCGAAAATCGACCCACTGGATCTGCa                     <  1:858057/44‑1 (MQ=21)
                                                |                                                         
GGTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTG  >  minE/373489‑373594

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