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 1,025,486 A→G 40.9% A82A (GCT→GCC)  hdhA ← 7alpha‑hydroxysteroid dehydrogenase, NAD‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,025,4860AG40.9% 22.4 / 46.1 66A82A (GCT→GCC) hdhA7alpha‑hydroxysteroid dehydrogenase, NAD‑dependent
Reads supporting (aligned to +/- strand):  ref base A (26/13);  new base G (17/10);  total (43/23)
Fisher's exact test for biased strand distribution p-value = 7.97e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAACGGTTTAGGTCCACCGCCACCGGCGTTGTTAACCAGAATATCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCACAACGGCAGGCA  >  minE/1025420‑1025543
                                                                  |                                                         
aaaCGGTTTAGGTCCACCGCCACCGGCGTTGTTAACCAGAATATCAACTTTACCCAGCTTACTGATAGc                                                         <  1:2707865/69‑1 (MQ=255)
aaaCGGTTTAGGTCCACCGCCACCGGCGTTGTTAACCAGAATATCAACTTTACCCAGCTTACTGATAGc                                                         <  1:1220791/69‑1 (MQ=255)
 aaCGGTTTAGGTCCACCGCCACCGGCGTTGTTAACCAGAATATCAACTTTACCCAGCTTACTGATAGc                                                         <  1:628410/68‑1 (MQ=255)
             ccaccgccaccgGCGTTGTTAACCAGAATATCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAg                                             >  1:2695353/1‑68 (MQ=255)
             ccaccgccaccgGCGTTGTTAACCAGAATATCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAg                                             >  1:2737798/1‑68 (MQ=255)
             ccaccgccaccgGCGTTGTTAACCAGAATATCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAg                                             >  1:2848682/1‑68 (MQ=255)
                     accgGCGTTGTTAACCAGGATATCAACTTTACCCAACTTACTGACGGCAAAGTCTGCCAGTGCagagag                                    <  1:1194372/69‑1 (MQ=37)
                     accgGCGTTGTTAACCAGGATATCAACTTTACCCAACTTACTGACGGCAAAGTCTGCCAGTGCagagag                                    <  1:1769435/69‑1 (MQ=37)
                              gttAACCAGAATATCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGtt                            >  1:2165210/1‑68 (MQ=255)
                              gttAACCAGAATATCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGtt                            >  1:1913017/1‑68 (MQ=255)
                              gttAACCAGAATATCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGtt                            >  1:1881633/1‑68 (MQ=255)
                              gttAACCAGAATATCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGtt                            >  1:3002181/1‑68 (MQ=255)
                              gttAACCAGAATATCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGtt                            >  1:1169616/1‑68 (MQ=255)
                                 aaCCAGGATATCAACTTTACCCAACTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCgg                         <  1:3106333/68‑1 (MQ=255)
                                 aaCCAGGATATCAACTTTACCCAACTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCgg                         <  1:2866312/68‑1 (MQ=255)
                                 aaCCAGGATATCAACTTTACCCAACTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCgg                         <  1:878867/68‑1 (MQ=255)
                                 aaCCAGGATATCAACTTTACCCAACTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCgg                         <  1:195489/68‑1 (MQ=255)
                                 aaCCAGGATATCAACTTTACCCAACTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCgg                         <  1:3251982/68‑1 (MQ=255)
                                 aaCCAGGATATCAACTTTACCCAACTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCgg                         <  1:3425196/68‑1 (MQ=255)
                                      gAATATCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTaa                   >  1:2227201/1‑69 (MQ=255)
                                      gAATATCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTaa                   >  1:330241/1‑69 (MQ=255)
                                        atatCGACTTTACCCAGCTTACTGATAGCAAAGTCTGcc                                               >  1:2451420/1‑39 (MQ=255)
                                        atatCAGCTTTACCCAGCTTACTGATAGCAAAGTCTGcc                                               >  1:6171/1‑39 (MQ=255)
                                        atatCAACTTTACCCAGCTTACTGATAGCAAAGTCTGcc                                               >  1:2114202/1‑39 (MQ=255)
                                        atatCAACTTTACCCAGCTTACTGATAGCAAAGTCTGcc                                               >  1:1720440/1‑39 (MQ=255)
                                         tatCAACTTTACCCAGCTTACTGATAGCAAAGTCTg                                                 >  1:1037429/1‑36 (MQ=255)
                                         tatCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAatat                >  1:3038472/1‑69 (MQ=255)
                                         tatCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAatat                >  1:1109793/1‑69 (MQ=255)
                                         tatCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAatat                >  1:2606782/1‑69 (MQ=255)
                                         tatCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAatat                >  1:246552/1‑69 (MQ=255)
                                         tatCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAatat                >  1:2114829/1‑69 (MQ=255)
                                         tatCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAatat                >  1:573834/1‑69 (MQ=255)
                                         tatCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAatat                >  1:2064045/1‑69 (MQ=255)
                                             aaCTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATcaca            >  1:1573228/1‑69 (MQ=255)
                                             aaCTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATcac             <  1:884470/68‑1 (MQ=255)
                                             aaCTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATcac             >  1:3252839/1‑68 (MQ=255)
                                                    cccAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCACAACggc       <  1:3236066/67‑1 (MQ=255)
                                                    cccAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCACAACggc       <  1:937714/67‑1 (MQ=255)
                                                    cccAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCACAACggc       <  1:2683295/67‑1 (MQ=255)
                                                      cAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCACAACggcagg    >  1:415805/1‑68 (MQ=255)
                                                       aGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCACAACggcaggca  <  1:824011/69‑1 (MQ=255)
                                                       aGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCACAACggcaggca  <  1:2556069/69‑1 (MQ=255)
                                                       aGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCACAACggcaggca  <  1:1429441/69‑1 (MQ=255)
                                                       aGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCACAACggcaggca  <  1:2270029/69‑1 (MQ=255)
                                                       aGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCACAACggcaggca  <  1:1559566/69‑1 (MQ=255)
                                                       aGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCACAACggcaggca  <  1:1741811/69‑1 (MQ=255)
                                                        acTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTcc                                >  1:1175067/2‑38 (MQ=25)
                                                        acTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCGCAGCggcaggca  >  1:1474168/2‑68 (MQ=255)
                                                        acTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCGCAGCggcaggca  >  1:736583/2‑68 (MQ=255)
                                                        acTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCGCAGCggcaggca  >  1:724803/2‑68 (MQ=255)
                                                        acTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCGCAGCggcaggca  >  1:656121/2‑68 (MQ=255)
                                                        acTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCGCAGCggcaggca  >  1:1589702/2‑68 (MQ=255)
                                                        acTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCGCAGCggcaggca  >  1:507080/2‑68 (MQ=255)
                                                        acTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCGCAGCggcaggca  >  1:462576/2‑68 (MQ=255)
                                                        acTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCGCAGCggcaggca  >  1:3423069/2‑68 (MQ=255)
                                                        acTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCGCAGCggcaggca  >  1:3367592/2‑68 (MQ=255)
                                                        acTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCGCAGCggcaggca  >  1:2111455/2‑68 (MQ=255)
                                                        acTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCGCAGCggcaggca  >  1:2115350/2‑68 (MQ=255)
                                                        acTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCGCAGCggcaggca  >  1:2247516/2‑68 (MQ=255)
                                                        acTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCGCAGCggcaggca  >  1:3109928/2‑68 (MQ=255)
                                                        acTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCGCAGCggcaggca  >  1:2453867/2‑68 (MQ=255)
                                                        acTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCGCAGCggcaggca  >  1:2895681/2‑68 (MQ=255)
                                                        acTTACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCGCAGCggcaggca  >  1:2662121/2‑68 (MQ=255)
                                                          ttACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCgg                         <  1:2095531/43‑1 (MQ=37)
                                                          ttACTGACGGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCgg                         <  1:2671177/43‑1 (MQ=37)
                                                               gATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAatat                >  1:2443449/1‑47 (MQ=255)
                                                                  |                                                         
AAACGGTTTAGGTCCACCGCCACCGGCGTTGTTAACCAGAATATCAACTTTACCCAGCTTACTGATAGCAAAGTCTGCCAGTGCAGAGAGTTCCTGTTCGGAAGTAATATCACAACGGCAGGCA  >  minE/1025420‑1025543

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