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 464,227 T→A 41.5% D28E (GAT→GAA)  sdhB → succinate dehydrogenase, FeS subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE464,2270TA41.5% 31.5 / 61.9 65D28E (GAT→GAA) sdhBsuccinate dehydrogenase, FeS subunit
Reads supporting (aligned to +/- strand):  ref base T (32/6);  new base A (10/17);  total (42/23)
Fisher's exact test for biased strand distribution p-value = 1.61e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TATAACCCGGATGTTGATGATGCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAGC  >  minE/464171‑464287
                                                        |                                                            
tataACCCGGATGTTGATGATGCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGa                                                   <  1:1122875/68‑1 (MQ=255)
tataACCCGGATGTTGATGATGCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGa                                                   <  1:1171206/68‑1 (MQ=255)
tataACCCGGATGTTGATGATGCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGa                                                   <  1:604316/68‑1 (MQ=255)
tataACCCGGATGTTGATGATGCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGa                                                   <  1:1264144/68‑1 (MQ=255)
            gTTGATGATGCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGctgctg                                      <  1:160103/69‑1 (MQ=255)
               gatgatGCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGAt                                   >  1:985970/1‑69 (MQ=255)
               gatgatGCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGAt                                   >  1:1793788/1‑69 (MQ=255)
               gatgatGCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGAt                                   >  1:546471/1‑69 (MQ=255)
               gatgatGCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGAt                                   >  1:1587652/1‑69 (MQ=255)
               gatgatGCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGAt                                   >  1:1159733/1‑69 (MQ=255)
                    tgCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTcgcg                                                    >  1:2328990/1‑47 (MQ=255)
                    tgCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCt                              >  1:716423/1‑69 (MQ=255)
                    tgCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCt                              >  1:3348860/1‑69 (MQ=255)
                    tgCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCt                              >  1:2741428/1‑69 (MQ=255)
                           cgTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATcc                         <  1:2925589/67‑1 (MQ=255)
                                 cAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTaa                   >  1:1480450/1‑67 (MQ=255)
                                 cAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTaa                   >  1:610379/1‑67 (MQ=255)
                                 cAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTaa                   >  1:96890/1‑67 (MQ=255)
                                 cAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTaa                   >  1:974140/1‑67 (MQ=255)
                                 cAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTaa                   >  1:431558/1‑67 (MQ=255)
                                 cAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTaa                   >  1:398070/1‑67 (MQ=255)
                                 cAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTaa                   >  1:3377841/1‑67 (MQ=255)
                                 cAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTaa                   >  1:2234041/1‑67 (MQ=255)
                                 cAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTa                    >  1:1055595/1‑66 (MQ=255)
                                 cAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGATaa                   >  1:2544083/1‑67 (MQ=255)
                                 cAGGATTACACCCTAGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTaa                   >  1:1262063/1‑67 (MQ=255)
                                      ttACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAaga               >  1:3271268/1‑66 (MQ=255)
                                      ttACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAaga               >  1:330986/1‑66 (MQ=255)
                                      ttACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAaga               >  1:1650151/1‑66 (MQ=255)
                                      ttACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAaga               >  1:2349463/1‑66 (MQ=255)
                                      ttACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAaga               >  1:2362094/1‑66 (MQ=255)
                                      ttACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAaga               >  1:288879/1‑66 (MQ=255)
                                      ttACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAaga               >  1:1718589/1‑66 (MQ=255)
                                        acacCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTaa                   >  1:2594964/1‑60 (MQ=255)
                                        acacCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTaa                   >  1:1830372/1‑60 (MQ=255)
                                        acacCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTaa                   >  1:1746848/1‑60 (MQ=255)
                                        acacCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTaa                   >  1:398401/1‑60 (MQ=255)
                                        acacCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTaa                   >  1:1971804/1‑60 (MQ=255)
                                           cccTGGAAGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGGAAGAt        >  1:3375203/1‑68 (MQ=255)
                                           cccTGGAAGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGAt        >  1:2192077/1‑68 (MQ=255)
                                           cccTGGAAGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGAt        >  1:840843/1‑68 (MQ=255)
                                           cccTGGAAGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGAt        >  1:872885/1‑68 (MQ=255)
                                           cccTGGAAGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGAt        >  1:959612/1‑68 (MQ=255)
                                           cccTGGAAGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGAt        >  1:315961/1‑68 (MQ=255)
                                           cccTGGAAGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGAt        >  1:3191684/1‑68 (MQ=255)
                                           cccTGGAAGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGAt        >  1:2165846/1‑68 (MQ=255)
                                           cccTGGAAGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGATGAAAGAGAAAGAt        >  1:1921481/1‑68 (MQ=255)
                                           cccTGCAAGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGAt        >  1:2239057/1‑68 (MQ=255)
                                                  aGCGGAAGATGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGTGAAAGATCCCAGc  <  1:3390465/67‑1 (MQ=255)
                                                  aGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGATCCCAGc  <  1:1037290/67‑1 (MQ=255)
                                                  aGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGATCCCAGc  <  1:1097082/67‑1 (MQ=255)
                                                  aGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGATCCCAGc  <  1:1157106/67‑1 (MQ=255)
                                                  aGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGATCCCAGc  <  1:2226435/67‑1 (MQ=255)
                                                  aGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGATCCCAGc  <  1:2154083/67‑1 (MQ=255)
                                                  aGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGATCCCAGc  <  1:81480/67‑1 (MQ=255)
                                                  aGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGATCCCAGc  <  1:769529/67‑1 (MQ=255)
                                                  aGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGATCCCAGc  <  1:1493266/67‑1 (MQ=255)
                                                  aGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGATCCCAGc  <  1:1570583/67‑1 (MQ=255)
                                                  aGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGATCCCAGc  <  1:2099582/67‑1 (MQ=255)
                                                  aGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGATCCCAGc  <  1:2799478/67‑1 (MQ=255)
                                                  aGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGATCCCAGc  <  1:2825482/67‑1 (MQ=255)
                                                  aGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGATCCCAGc  <  1:2874834/67‑1 (MQ=255)
                                                  aGCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGATCCCAGc  <  1:1756769/67‑1 (MQ=255)
                                                   gCGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGATCCCAGc  <  1:342497/66‑1 (MQ=255)
                                                    cGGAAGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATTCAGCTGAAAGAGAAAGATCCCAGc  <  1:839980/65‑1 (MQ=255)
                                                        |                                                            
TATAACCCGGATGTTGATGATGCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAGC  >  minE/464171‑464287

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