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 373,549 G→A 23.7% E133E (GAG→GAA)  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
*minE373,5490GA23.7% 144.0 / 35.8 110E133E (GAG→GAA) fepEregulator of length of O‑antigen component of lipopolysaccharide chains
Reads supporting (aligned to +/- strand):  ref base G (59/24);  new base A (8/18);  total (67/43)
Fisher's exact test for biased strand distribution p-value = 4.04e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 125 total aligned reads displayed.

GGTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGTT  >  minE/373489‑373615
                                                            |                                                                  
ggTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGaaaa                                                             >  1:2023772/1‑68 (MQ=255)
ggTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGaaaa                                                             >  1:227277/1‑68 (MQ=255)
ggTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGaaaa                                                             >  1:1844082/1‑68 (MQ=255)
ggTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGaaaa                                                             >  1:3331326/1‑68 (MQ=255)
  ttAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATc                                                           <  1:61965/68‑1 (MQ=255)
   tAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcg                                                          >  1:1795268/1‑68 (MQ=255)
   tAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcg                                                          >  1:244929/1‑68 (MQ=255)
   tAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcg                                                          >  1:1577565/1‑68 (MQ=255)
   tAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcg                                                          >  1:3363131/1‑68 (MQ=255)
   tAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATc                                                           >  1:1625959/1‑67 (MQ=255)
                 agTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGc                                           <  1:1027761/69‑1 (MQ=255)
                 agTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGc                                           <  1:1107463/69‑1 (MQ=255)
                 agTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGc                                           <  1:79417/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTTAAAGAAGCGAAAATCGACCCACTGGATCTGCa                                          <  1:2831428/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                                          <  1:479373/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                                          <  1:101392/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                                          <  1:1454295/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                                          <  1:839557/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                                          <  1:2769417/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                                          <  1:1195702/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                                          <  1:1592560/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                                          <  1:2757906/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                                          <  1:2412929/69‑1 (MQ=255)
                  gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa                                          <  1:2644204/69‑1 (MQ=255)
                   tACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCAt                                         >  1:1843938/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                                      >  1:875730/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                                      >  1:2429065/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                                      >  1:832966/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                                      <  1:2705010/54‑1 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                                      >  1:3074205/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                                      >  1:602756/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                                      >  1:546724/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                                      >  1:3374615/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                                      >  1:373533/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                                      <  1:1245647/54‑1 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                                      >  1:1231593/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga                                                      >  1:1618448/1‑54 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacca                                                      <  1:643057/54‑3 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCAt                                         >  1:2049714/1‑67 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg                                       >  1:2179367/1‑69 (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                                       >  1:2662145/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg                                       >  1:347173/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg                                       >  1:2050860/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg                                       >  1:1876394/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg                                       >  1:1500968/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg                                       >  1:3262185/1‑69 (MQ=255)
                     ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATc                                        >  1:1779859/1‑68 (MQ=255)
                       tGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcgc                                      >  1:48746/1‑68 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc                                    >  1:1544905/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc                                    >  1:1127555/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc                                    >  1:313586/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc                                    <  1:1349102/69‑1 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc                                    >  1:288359/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc                                    >  1:2876191/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc                                    <  1:3387097/69‑1 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc                                    <  1:44285/69‑1 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc                                    <  1:1718465/69‑1 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc                                    >  1:2157912/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc                                    >  1:1687716/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc                                    >  1:2685707/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc                                    >  1:484610/1‑69 (MQ=255)
                        gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc                                    <  1:2588065/69‑1 (MQ=255)
                           ttCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCa                                   <  1:2732224/67‑1 (MQ=255)
                           ttCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCa                                   <  1:3123218/67‑1 (MQ=255)
                           ttCATCACCTTATGCGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAAt                                 <  1:186153/69‑1 (MQ=255)
                             catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg                               >  1:653184/1‑69 (MQ=255)
                             catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg                               >  1:472056/1‑69 (MQ=255)
                             catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg                               >  1:1127733/1‑69 (MQ=255)
                             catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg                               >  1:1923087/1‑69 (MQ=255)
                             catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg                               >  1:3104746/1‑69 (MQ=255)
                             catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg                               >  1:2840410/1‑69 (MQ=255)
                                caCCTTATGTGATGGATCAATTAAAAGAAGCGATAATCGACCCACTGGATCTGCa                                          <  1:2664771/55‑1 (MQ=255)
                                caCCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCTCAATTGTCg                            <  1:373303/69‑1 (MQ=255)
                                caCCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCg                            <  1:1914623/69‑1 (MQ=255)
                                caCCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCg                            <  1:1744742/69‑1 (MQ=255)
                                     tATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTg                       >  1:1416194/1‑69 (MQ=255)
                                     tATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTg                       >  1:1053526/1‑69 (MQ=255)
                                     tATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTg                       >  1:2145637/1‑69 (MQ=255)
                                     tATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTg                       >  1:1297706/1‑69 (MQ=255)
                                     tATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTg                       >  1:1508458/1‑69 (MQ=255)
                                       tgtgATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCg                            <  1:784554/62‑1 (MQ=255)
                                           aTGGATCAATTAAAAGACGCGAAAATCGACCCACTGGATCTGCa                                          <  1:858057/44‑1 (MQ=21)
                                                      aaaaGAGGCGAAAATCGACGAACTGGATTTGCATCGCGTAATTGTCGCATTGAGCGAAAAAATGAAAGc      >  1:1330454/1‑69 (MQ=255)
                                                      aaaaGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGc      >  1:3382077/1‑69 (MQ=255)
                                                          gagTCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt  <  1:1230073/69‑1 (MQ=255)
                                                          gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCTAAAAAATGAAAGCGGtt  <  1:3257639/69‑1 (MQ=255)
                                                          gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt  <  1:2294863/69‑1 (MQ=255)
                                                          gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt  <  1:2161973/69‑1 (MQ=255)
                                                          gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt  <  1:1414444/69‑1 (MQ=255)
                                                          gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt  <  1:659153/69‑1 (MQ=255)
                                                          gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt  <  1:254274/69‑1 (MQ=255)
                                                          gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt  <  1:117502/69‑1 (MQ=255)
                                                          gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt  <  1:1978313/69‑1 (MQ=255)
                                                          gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt  <  1:3332300/69‑1 (MQ=255)
                                                          gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt  <  1:1704676/69‑1 (MQ=255)
                                                          gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt  <  1:280324/69‑1 (MQ=255)
                                                            |                                                                  
GGTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGTT  >  minE/373489‑373615

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A